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Conserved domains on  [gi|1079631681|emb|SCW44360|]
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simple sugar transport system substrate-binding protein [Ruminococcaceae bacterium YRB3002]

Protein Classification

ABC transporter substrate-binding protein( domain architecture ID 10156879)

ABC transporter substrate-binding protein similar to the Escherichia coli ABC transporter periplasmic-binding protein YtfQ, which is up-regulated under glucose-limited conditions and is homologous to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily; may be involved in the transport of sugar-containing molecules across cellular and organellar membranes

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
40-325 2.13e-114

periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.


:

Pssm-ID: 380532 [Multi-domain]  Cd Length: 285  Bit Score: 332.65  E-value: 2.13e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTnDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06309     1 TVGFSQAGSESPWRVANTKSIKEAAK-KRGYELVYTDANQDQEKQINDIRDLIAQGVDAILISPIDATGWDPVLKEAKDA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyVNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd06309    80 GIPVILVDRTIDGEDGSLYVTFIGSDFVEEGRRAAEWLVKNYKGGK-GNVVELQGTAGSSVAIDRSKGFREVIKKHPNIK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKN-KDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTALQYCLDGKI 278
Cdd:cd06309   159 IVASQSGNFTREKGQKVMENLLQAGpGDIDVIYAHNDDMALGAIQALKEAGLKPGK--DVLVVGIDGQKDALEAIKAGEL 236
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 279 SLCVECNPMHGPLVEQLIKRYRSGETIPKHVFIDEAAFTREDLTQEM 325
Cdd:cd06309   237 NATVECNPLFGPTAFDTIAKLLAGEKVPKLIIVEERLFDKDNAAEEL 283
 
Name Accession Description Interval E-value
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
40-325 2.13e-114

periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.


Pssm-ID: 380532 [Multi-domain]  Cd Length: 285  Bit Score: 332.65  E-value: 2.13e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTnDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06309     1 TVGFSQAGSESPWRVANTKSIKEAAK-KRGYELVYTDANQDQEKQINDIRDLIAQGVDAILISPIDATGWDPVLKEAKDA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyVNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd06309    80 GIPVILVDRTIDGEDGSLYVTFIGSDFVEEGRRAAEWLVKNYKGGK-GNVVELQGTAGSSVAIDRSKGFREVIKKHPNIK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKN-KDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTALQYCLDGKI 278
Cdd:cd06309   159 IVASQSGNFTREKGQKVMENLLQAGpGDIDVIYAHNDDMALGAIQALKEAGLKPGK--DVLVVGIDGQKDALEAIKAGEL 236
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 279 SLCVECNPMHGPLVEQLIKRYRSGETIPKHVFIDEAAFTREDLTQEM 325
Cdd:cd06309   237 NATVECNPLFGPTAFDTIAKLLAGEKVPKLIIVEERLFDKDNAAEEL 283
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
6-321 5.78e-73

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 227.89  E-value: 5.78e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681   6 KTLSVLITLLLMIGVFTSGCSDTPDAKTGDKEFYVIGFSQLGSESDWRIANTKSMsQTFTNDNGYELIIENAKQQQDNQF 85
Cdd:COG1879     1 KRLALLAAVLALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGA-EAAAKELGVELIVVDAEGDAAKQI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  86 AAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSe 165
Cdd:COG1879    80 SQIEDLIAQGVDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDV---DGSDRVAYVGSDNYAAGRLAAEYLAKALGGK- 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 166 yVNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRAL 245
Cdd:COG1879   156 -GKVAILTGSPGAPAANERTDGFKEALKEYPGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFAANDGMALGAAQAL 234
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1079631681 246 DEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVEQLIKRYRSGETIPKHVFIDEAAFTREDL 321
Cdd:COG1879   235 KAAGRK----GDVKVVGFDGSPEALQAIKDGTIDATVAQDPyLQGYLAVDAALKLLKGKEVPKEILTPPVLVTKENV 307
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
41-279 9.98e-37

Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433182 [Multi-domain]  Cd Length: 259  Bit Score: 132.43  E-value: 9.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  41 IGFSQLGSESDWRIANTKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAG 120
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAKELGGEVIVVGPAEADAAEQVAQIEDAIAQGVDAIIVAPVDPTALAPVLKKAKDAG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 121 IPVIIIDrSVAVRNDDLYltNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDA-ESTHSNWK 199
Cdd:pfam13407  81 IPVVTFD-SDAPSSPRLA--YVGFDNEAAGEAAGELLAEALGGK--GKVAILSGSPGDPNANERIDGFKKVlKEKYPGIK 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVA-QLYGDFTEAKGYEVMTEYLKKNKD-IDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGK 277
Cdd:pfam13407 156 VVAeVEGTNWDPEKAQQQMEALLTAYPNpLDGIISPNDGMAGGAAQALEAAGLA----GKVVVTGFDATPEALEAIKDGT 231

                  ..
gi 1079631681 278 IS 279
Cdd:pfam13407 232 ID 233
PRK10653 PRK10653
ribose ABC transporter substrate-binding protein RbsB;
58-312 1.89e-18

ribose ABC transporter substrate-binding protein RbsB;


Pssm-ID: 182620 [Multi-domain]  Cd Length: 295  Bit Score: 83.99  E-value: 1.89e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  58 KSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEegwDMILNEVQSA---GIPVIIIDRsVAVRN 134
Cdd:PRK10653   45 KDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDS---DAVGNAVKMAnqaNIPVITLDR-GATKG 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 135 DdlYLTNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLYGDFTEAKGY 214
Cdd:PRK10653  121 E--VVSHIASDNVAGGKMAGDFIAKKLGEG--AKVIQLEGIAGTSAARERGEGFKQAVAAH-KFNVLASQPADFDRTKGL 195
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 215 EVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygengQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVE 293
Cdd:PRK10653  196 NVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKS-----DVMVVGFDGTPDGIKAVNRGKLAATIAQQPdQIGAIGV 270
                         250
                  ....*....|....*....
gi 1079631681 294 QLIKRYRSGETIPKHVFID 312
Cdd:PRK10653  271 ETADKVLKGEKVEAKIPVD 289
 
Name Accession Description Interval E-value
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
40-325 2.13e-114

periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.


Pssm-ID: 380532 [Multi-domain]  Cd Length: 285  Bit Score: 332.65  E-value: 2.13e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTnDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06309     1 TVGFSQAGSESPWRVANTKSIKEAAK-KRGYELVYTDANQDQEKQINDIRDLIAQGVDAILISPIDATGWDPVLKEAKDA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyVNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd06309    80 GIPVILVDRTIDGEDGSLYVTFIGSDFVEEGRRAAEWLVKNYKGGK-GNVVELQGTAGSSVAIDRSKGFREVIKKHPNIK 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKN-KDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTALQYCLDGKI 278
Cdd:cd06309   159 IVASQSGNFTREKGQKVMENLLQAGpGDIDVIYAHNDDMALGAIQALKEAGLKPGK--DVLVVGIDGQKDALEAIKAGEL 236
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 279 SLCVECNPMHGPLVEQLIKRYRSGETIPKHVFIDEAAFTREDLTQEM 325
Cdd:cd06309   237 NATVECNPLFGPTAFDTIAKLLAGEKVPKLIIVEERLFDKDNAAEEL 283
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
6-321 5.78e-73

ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism];


Pssm-ID: 441483 [Multi-domain]  Cd Length: 307  Bit Score: 227.89  E-value: 5.78e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681   6 KTLSVLITLLLMIGVFTSGCSDTPDAKTGDKEFYVIGFSQLGSESDWRIANTKSMsQTFTNDNGYELIIENAKQQQDNQF 85
Cdd:COG1879     1 KRLALLAAVLALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGA-EAAAKELGVELIVVDAEGDAAKQI 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  86 AAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSe 165
Cdd:COG1879    80 SQIEDLIAQGVDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDV---DGSDRVAYVGSDNYAAGRLAAEYLAKALGGK- 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 166 yVNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRAL 245
Cdd:COG1879   156 -GKVAILTGSPGAPAANERTDGFKEALKEYPGIKVVAEQYADWDREKALEVMEDLLQAHPDIDGIFAANDGMALGAAQAL 234
                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1079631681 246 DEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVEQLIKRYRSGETIPKHVFIDEAAFTREDL 321
Cdd:COG1879   235 KAAGRK----GDVKVVGFDGSPEALQAIKDGTIDATVAQDPyLQGYLAVDAALKLLKGKEVPKEILTPPVLVTKENV 307
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
40-312 5.73e-55

periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins.


Pssm-ID: 380478 [Multi-domain]  Cd Length: 268  Bit Score: 180.45  E-value: 5.73e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTnDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd01536     1 KIGVVVKDLTNPFWVAVKKGAEAAAK-ELGVELVVLDAQGDVAKQISQIEDLIAQGVDAIIIAPVDSEALVPAVKKANAA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAvrNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd01536    80 GIPVVAVDTDID--GGGDVVAFVGTDNYEAGKLAGEYLAEALGGK--GKVAILEGPPGSSTAIDRTKGFKEALKKYPDIE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKIS 279
Cdd:cd01536   156 IVAEQPANWDRAKALTVTENLLQANPDIDAVFAANDDMALGAAEALKAAGRT----GDIKIVGVDGTPEALKAIKDGELD 231
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1079631681 280 LCVECNP-MHGPLVEQLIKRYRSGETIPKHVFID 312
Cdd:cd01536   232 ATVAQDPyLQGYLAVEAAVKLLNGEKVPKEILTP 265
PBP1_sensor_kinase-like cd06308
periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic ...
40-312 1.67e-53

periplasmic binding domain of two-component sensor kinase signaling systems; Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.


Pssm-ID: 380531 [Multi-domain]  Cd Length: 268  Bit Score: 176.58  E-value: 1.67e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06308     1 VIGFSQCSLNDPWRAAMNEEIKAEAAKYPNVELIVTDAQGDAAKQIADIEDLIAQGVDLLIVSPNEADALTPVVKKAYDA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd06308    81 GIPVIVLDRKV---SGDDYTAFIGADNVEIGRQAGEYIAELLNGKG--NVVEIQGLPGSSPAIDRHKGFLEAIAKYPGIK 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTAL-QYCLDGKI 278
Cdd:cd06308   156 IVASQDGDWLRDKAIKVMEDLLQAHPDIDAVYAHNDEMALGAYQALKKAGR----EKEIKIIGVDGLPEAGeKAVKDGIL 231
                         250       260       270
                  ....*....|....*....|....*....|....
gi 1079631681 279 SLCVEcNPMHGPLVEQLIKRYRSGETIPKHVFID 312
Cdd:cd06308   232 AATFL-YPTGGKEAIEAALKILNGEKVPKEIVLP 264
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
69-312 2.06e-42

periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs; Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis D-ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group belong to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.


Pssm-ID: 380546 [Multi-domain]  Cd Length: 268  Bit Score: 147.83  E-value: 2.06e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLH 148
Cdd:cd06323    29 GVELVVLDAQNDPAKQLSQVEDLIVRKVDALLINPTDSDAVSPAVEEANEAGIPVITVDRSV---TGGKVVSHIASDNVA 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 149 QGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDID 228
Cdd:cd06323   106 GGEMAAEYIAKKLGGKG--KVVELQGIPGTSAARERGKGFHNAIAKYPKINVVASQTADFDRTKGLNVMENLLQAHPDID 183
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 229 VLYSENDNMTFGAMRALDEAGITygengQVKIITFDATKTALQYCLDGKISLCVECNP--MHGPLVEQLIKrYRSGETIP 306
Cdd:cd06323   184 AVFAHNDEMALGAIQALKAAGRK-----DVIVVGFDGTPDAVKAVKDGKLAATVAQQPeeMGAKAVETADK-YLKGEKVP 257

                  ....*.
gi 1079631681 307 KHVFID 312
Cdd:cd06323   258 KKIPVP 263
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
40-320 7.88e-37

periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380541 [Multi-domain]  Cd Length: 282  Bit Score: 133.69  E-value: 7.88e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTfTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06318     1 KIGFSQRTLASPYYAALVAAAKAE-AKKLGVELVVTDAQNDLTKQISDVEDLITRGVDVLILNPVDPEGLTPAVKAAKAA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDdlYLTNIGSDFLHQGELAVEWLEDqTSDSEYVNILHLQGTYGATAQLMRT----KAIEDA---E 192
Cdd:cd06318    80 GIPVITVDSALDPSAN--VATQVGRDNKQNGVLVGKEAAK-ALGGDPGKIIELSGDKGNEVSRDRRdgflAGVNEYqlrK 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 193 STHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQY 272
Cdd:cd06318   157 YGKSNIKVVAQPYGNWIRSGAVAAMEDLLQAHPDINVVYAENDDMALGAMKALKAAGML----DKVKVAGADGQKEALKL 232
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|
gi 1079631681 273 CLDGKISLCVECNP--MHGPLVEQLIKRYRSGETIPKHVFIDEAAFTRED 320
Cdd:cd06318   233 IKDGKYVATGLNDPdlLGKTAVDTAAKVVKGEESFPEFTYTPTALITKDN 282
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
41-279 9.98e-37

Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 433182 [Multi-domain]  Cd Length: 259  Bit Score: 132.43  E-value: 9.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  41 IGFSQLGSESDWRIANTKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAG 120
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAKELGGEVIVVGPAEADAAEQVAQIEDAIAQGVDAIIVAPVDPTALAPVLKKAKDAG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 121 IPVIIIDrSVAVRNDDLYltNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDA-ESTHSNWK 199
Cdd:pfam13407  81 IPVVTFD-SDAPSSPRLA--YVGFDNEAAGEAAGELLAEALGGK--GKVAILSGSPGDPNANERIDGFKKVlKEKYPGIK 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVA-QLYGDFTEAKGYEVMTEYLKKNKD-IDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGK 277
Cdd:pfam13407 156 VVAeVEGTNWDPEKAQQQMEALLTAYPNpLDGIISPNDGMAGGAAQALEAAGLA----GKVVVTGFDATPEALEAIKDGT 231

                  ..
gi 1079631681 278 IS 279
Cdd:pfam13407 232 ID 233
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
40-302 3.20e-35

periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380623 [Multi-domain]  Cd Length: 271  Bit Score: 129.04  E-value: 3.20e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTfTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd19968     1 KIGFSFPNLSFPFFVYMHEQAVDE-AAKLGVKLVVLDAQNSSSKQASDLENAIAQGVDGIIVSPIDVKALVPAIEAAIKA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVrndDLYLTNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd19968    80 GIPVVTVDRRAEG---AAPVPHVGADNVAGGREVAKFVVDKLPNG--AKVIELTGTPGSSPAIDRTKGFHEELAAGPKIK 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKNK-DIDVLYSENDNMTFGAMRALDEAGItygENGQVKIITFDATKTALQYCLDGKI 278
Cdd:cd19968   155 VVFEQTGNFERDEGLTVMENILTSLPgPPDAIICANDDMALGAIEAMRAAGL---DLKKVKVIGFDAVPDALQAIKDGEL 231
                         250       260
                  ....*....|....*....|....*.
gi 1079631681 279 SLCVECNP--MHGPLVEQLIKRYRSG 302
Cdd:cd19968   232 YATVEQPPggQARTALRILVDYLKDK 257
PBP1_rhizopine_binding-like cd06301
periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to ...
39-282 7.53e-35

periplasmic binding proteins specific to rhizopines; Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily.


Pssm-ID: 380524 [Multi-domain]  Cd Length: 272  Bit Score: 128.12  E-value: 7.53e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  39 YVIGFSQLGSESDWRIANTKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQS 118
Cdd:cd06301     1 IKIGVSMQNFSDEFLTYLRDAIEAYAKEYPGVKLVIVDAQSDAAKQLSQVENFIAQGVDAIIVNPVDTDASAPAVDAAAD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 119 AGIPVIIIDRSVAvrNDDLYLTNIGSDFLHQGELAVEWLEDQTSdsEYVNILHLQGTYGATAQLMRTKAIEDAESTHSNW 198
Cdd:cd06301    81 AGIPLVYVNREPD--SKPKGVAFVGSDDIESGELQMEYLAKLLG--GKGNIAILDGVLGHEAQILRTEGNKDVLAKYPGM 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 199 KIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKI 278
Cdd:cd06301   157 KIVAEQTANWSREKAMDIVENWLQSGDKIDAIVANNDEMAIGAILALEAAGKK----DDILVAGIDATPDALKAMKAGRL 232

                  ....
gi 1079631681 279 SLCV 282
Cdd:cd06301   233 DATV 236
PBP1_ABC_ThpA_XypA cd06313
periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group ...
41-319 2.44e-33

periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems; This group includes periplasmic D-threitol-binding protein ThpA and xylitol/L-sorbitol-binding protein XypA, which are part of sugar ABC-type transport systems. Both ThpA and XypA share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge.


Pssm-ID: 380536 [Multi-domain]  Cd Length: 277  Bit Score: 124.30  E-value: 2.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  41 IGFSQLGSESDWRIANTKSMsQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAG 120
Cdd:cd06313     2 IGFTVYGLSSEFITNLVEAM-KAVAKELNVDLVVLDGNGDVSTQINQVDTLIAQGVDAIIVVPVDADALAPAVEKAKEAG 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 121 IPVIIidrSVAVRNDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWKI 200
Cdd:cd06313    81 IPLVG---VNALIENEDLTAYVGSDDVVAGELEGQAVADRLGGKG--NVVILEGPIGQSAQIDRGKGIENVLKKYPDIKV 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 201 VAQLYGDFTEAKGYEVMTEYLKKNKD-IDVLYSENDNMTFGAMRALDEAGITygengQVKIITFDATKTALQYCLDGKIS 279
Cdd:cd06313   156 LAEQTANWSRDEAMSLMENWLQAYGDeIDGIIAQNDDMALGALQAVKAAGRD-----DIPVVGIDGIEDALQAVKSGELI 230
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1079631681 280 LCVECN-PMHGPLVEQLIKRYRSGETIPKHVFIDEAAFTRE 319
Cdd:cd06313   231 ATVLQDaEAQGKGAVEVAVDAVKGEGVEKKYYIPFVLVTKD 271
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
40-317 3.16e-31

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380545 [Multi-domain]  Cd Length: 270  Bit Score: 118.15  E-value: 3.16e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTnDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd06322     1 TIGVSLLTLQHPFFVDIKDAMKKEAA-ELGVKVVVADANGDLAKQLSQIEDFIQQGVDAIILAPVDSGGIVPAIEAANEA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDrsvAVRNDDLYLTNIGSDFLHQGELAVEWLEDqtsdseyvNILHLQGTYG------ATAQLMRTKAIEDAES 193
Cdd:cd06322    80 GIPVFTVD---VKADGAKVVTHVGTDNYAGGKLAGEYALK--------ALLGGGGKIAiidypeVESVVLRVNGFKEAIK 148
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 194 THSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAgityGENGQVKIITFDATKTALQYC 273
Cdd:cd06322   149 KYPNIEIVAEQPGDGRREEALAATEDMLQANPDLDGIFAIGDPAALGALTAIESA----GKEDKIKVIGFDGNPEAIKAI 224
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 274 L-DGKISLCVECNP--MHGPLVEQLIKrYRSGETIPKHVFIDEAAFT 317
Cdd:cd06322   225 AkGGKIKADIAQQPdkIGQETVEAIVK-YLAGETVEKEILIPPKLYT 270
PBP1_ABC_sugar_binding-like cd19999
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
40-272 3.18e-29

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380654 [Multi-domain]  Cd Length: 313  Bit Score: 113.94  E-value: 3.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWR---IANTKSMSQTFTNDnGY--ELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILN 114
Cdd:cd19999     1 VIGVSNGYVGNEWRaqmIADFEEVAAEYKEE-GVisDLIVQNADADATGQISQIRNMINEGVDAILIDPVSATALNPVIE 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 115 EVQSAGIPVIIIDRSVAvrNDDLYltNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAEST 194
Cdd:cd19999    80 KAQAAGILVVSFDQPVS--SPDAI--NVVIDQYKWAAIQAQWLAEQLGGKG--NIVAINGVAGNPANEARVKAADDVFAK 153
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079631681 195 HSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSEnDNMTFGAMRALDEAGItygengQVKIITFDATKTALQY 272
Cdd:cd19999   154 YPGIKVLASVPGGWDQATAQQVMATLLATYPDIDGVLTQ-DGMAEGVLRAFQAAGK------DPPVMTGDYRKGFLRK 224
PBP1_ABC_sugar_binding-like cd19996
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
40-330 1.22e-28

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380651 [Multi-domain]  Cd Length: 302  Bit Score: 112.33  E-value: 1.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMSQTFTN--DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQ 117
Cdd:cd19996     1 TIGFSNAGLGNSWRVQMIAEFEAEAAKlkKLIKELIYTDAQGDTQKQIADIQDLIAQGVDAIIVSPNSPTALLPAIEKAA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 118 SAGIPVIIIDRSVAVRNddlYLTNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSN 197
Cdd:cd19996    81 AAGIPVVLFDSGVGSDK---YTAFVGVDDAAFGRVGAEWLVKQLGGKG--NIIALRGIAGVSVSEDRWAGAKEVFKEYPG 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 198 WKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAG-----ITyGENGQvkiitfDATKTALQy 272
Cdd:cd19996   156 IKIVGEVYADWDYAKAKQAVESLLAAYPDIDGVWSDGGAMTLGAIEAFEEAGrplvpMT-GEDNN------GFLKAWKE- 227
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1079631681 273 cLDGKISLCVECNPMHGPL-VEQLIKRYRsGETIPKHVFIDEAAFTREDLTQEMVEERD 330
Cdd:cd19996   228 -LPGFKSIAPSYPPWLGATaLDAALAALE-GEPVPKYVYIPLPVITDENLDQYVKPDLD 284
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
67-309 1.36e-28

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380533 [Multi-domain]  Cd Length: 272  Bit Score: 111.28  E-value: 1.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDN--QFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGS 144
Cdd:cd06310    27 DLGVKIIFVGPESEEDVagQNSLLEELINKKPDAIVVAPLDSEDLVDPLKDAKDKGIPVIVIDSGI---KGDAYLSYIAT 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 DFLHQGELAVEWLEDQTSDSEYVNILhlQGTYGATAQLMRTKAIEDAESTHSN-WKIVAQLYGDFTEAKGYEVMTEYLKK 223
Cdd:cd06310   104 DNYAAGRLAAQKLAEALGGKGKVAVL--SLTAGNSTTDQREEGFKEYLKKHPGgIKVLASQYAGSDYAKAANETEDLLGK 181
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 224 NKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNPMH-GPLVEQLIKRYRSG 302
Cdd:cd06310   182 YPDIDGIFATNEITALGAAVAIKSRKLS----GQIKIVGFDSQEELLDALKNGKIDALVVQNPYEiGYEGIKLALKLLKG 257

                  ....*..
gi 1079631681 303 ETIPKHV 309
Cdd:cd06310   258 EEVPKNI 264
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
65-278 2.00e-28

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380625 [Multi-domain]  Cd Length: 275  Bit Score: 110.80  E-value: 2.00e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  65 TNDNGYELIIENAKQQQD--NQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDrsvaVRNDD------ 136
Cdd:cd19970    26 KEANGYELLVKGIKQETDieQQIAIVENLIAQKVDAIVIAPADSKALVPVLKKAVDAGIAVINID----NRLDAdalkeg 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 137 -LYLTNIGSDFLHQGELAVEWLEDQTSDSEYVNILhlQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLYGDFTEAKGYE 215
Cdd:cd19970   102 gINVPFVGPDNRQGAYLAGDYLAKKLGKGGKVAII--EGIPGADNAQQRKAGFLKAFEEA-GMKIVASQSANWEIDEANT 178
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1079631681 216 VMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKI 278
Cdd:cd19970   179 VAANLLTAHPDIRGILCANDNMALGAIKAVDAAGKA----GKVLVVGFDNIPAVRPLLKDGKM 237
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
66-312 5.12e-28

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380626 [Multi-domain]  Cd Length: 267  Bit Score: 109.60  E-value: 5.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAvrNDDLYLTNIGSD 145
Cdd:cd19971    26 EANGDELITRDPQLDQNKQNEQIEDMINQGVDAIFLNPVDSEGIRPALEAAKEAGIPVINVDTPVK--DTDLVDSTIASD 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQTSDSEYVNILHLQgtyGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNK 225
Cdd:cd19971   104 NYNAGKLCGEDMVKKLPEGAKIAVLDHP---TAESCVDRIDGFLDAIKKNPKFEVVAQQDGKGQLEVAMPIMEDILQAHP 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 226 DIDVLYSENDNMTFGAMRALDEAgityGENGQVKIITFDATKTALQYCLDGKISLCVECNPMH-GPLVEQLIKRYRSGET 304
Cdd:cd19971   181 DLDAVFALNDPSALGALAALKAA----GKLGDILVYGVDGSPDAKAAIKDGKMTATAAQSPIEiGKKAVETAYKILNGEK 256

                  ....*...
gi 1079631681 305 IPKHVFID 312
Cdd:cd19971   257 VEKEIVVP 264
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
68-321 3.63e-27

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380542 [Multi-domain]  Cd Length: 278  Bit Score: 107.83  E-value: 3.63e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDrsVAVRNDDlYLTNIGSDFL 147
Cdd:cd06319    28 LGYEFVTYDQKNSANEQVTNANDLIAQGVDGIIISPTNSSAAPTVLDLANEAKIPVVIAD--IGTGGGD-YVSYIISDNY 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 148 HQGELAVEWL-----EDQTSDSEYVNI-LHLQGTYGATaqlmRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYL 221
Cdd:cd06319   105 DGGYQAGEYLaealkENGWGGGSVGIIaIPQSRVNGQA----RTAGFEDALEEAGVEEVALRQTPNSTVEETYSAAQDLL 180
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 222 KKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNPM-HGPLVEQLIKRYR 300
Cdd:cd06319   181 AANPDIKGIFAQNDQMAQGALQAIEEAGRT----GDILVVGFDGDPEALDLIKDGKLDGTVAQQPFgMGARAVELAIQAL 256
                         250       260
                  ....*....|....*....|..
gi 1079631681 301 SGETIP-KHVFIDEAAFTREDL 321
Cdd:cd06319   257 NGDNTVeKEIYLPVLLVTSENV 278
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
75-310 1.17e-24

periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis; Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.


Pssm-ID: 380543 [Multi-domain]  Cd Length: 283  Bit Score: 100.80  E-value: 1.17e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  75 ENAKQQQDNQFAAIrrfILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDL----YLTNIGSDFLHQG 150
Cdd:cd06320    40 ETDTQGQLNLLETM---LNKGYDAILVSPISDTNLIPPIEKANKKGIPVINLDDAVDADALKKaggkVTSFIGTDNVAAG 116
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 151 ELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVL 230
Cdd:cd06320   117 ALAAEYIAEKLPGGG--KVAIIEGLPGNAAAEARTKGFKETFKKAPGLKLVASQPADWDRTKALDAATAILQAHPDLKGI 194
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 231 YSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVEQLIKRYRSGETIPKHV 309
Cdd:cd06320   195 YAANDTMALGAVEAVKAAGKT----GKVLVVGTDGIPEAKKSIKAGELTATVAQYPyLEGAMAVEAALRLLQGQKVPAVV 270

                  .
gi 1079631681 310 F 310
Cdd:cd06320   271 A 271
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
82-318 2.44e-23

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380661 [Multi-domain]  Cd Length: 274  Bit Score: 97.28  E-value: 2.44e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  82 DNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQT 161
Cdd:cd20006    46 DGQIELIEEAIAQKPDAIVLAASDYDRLVEAVERAKKAGIPVITIDSPV---NSKKADSFVATDNYEAGKKAGEKLASLL 122
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 162 SDSEYVNIL-HLQGTygaTAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFG 240
Cdd:cd20006   123 GEKGKVAIVsFVKGS---STAIEREEGFKQALAEYPNIKIVETEYCDSDEEKAYEITKELLSKYPDINGIVALNEQSTLG 199
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 241 AMRALDEAGItygeNGQVKIITFDATKTALQYCLDGKISLCVECNP--MhGPL-VEQLIKRYRsGETIPKHVFIDEAAFT 317
Cdd:cd20006   200 AARALKELGL----GGKVKVVGFDSSVEEIQLLEEGIIDALVVQNPfnM-GYLsVQAAVDLLN-GKKIPKRIDTGSVVIT 273

                  .
gi 1079631681 318 R 318
Cdd:cd20006   274 K 274
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
66-264 2.72e-23

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 98.35  E-value: 2.72e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEgwDMILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSD 145
Cdd:COG1609    88 RERGYQLLLANSDEDPEREREALRLLLSRRVDGLILAGSRLD--DARLERLAEAGIPVVLIDRPL----PDPGVPSVGVD 161
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQL--YGDFTEAKGYEVMTEYLKK 223
Cdd:COG1609   162 NRAGARLATEHLIELG----HRRIAFIGGPADSSSARERLAGYREALAEA-GLPPDPELvvEGDFSAESGYEAARRLLAR 236
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1079631681 224 NKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:COG1609   237 GPRPTAIFCANDLMALGALRALREAGLRVPE--DVSVVGFD 275
PBP1_GGBP cd01539
periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and ...
57-279 6.58e-23

periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species; Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380481 [Multi-domain]  Cd Length: 302  Bit Score: 96.50  E-value: 6.58e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  57 TKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAV---- 132
Cdd:cd01539    19 RKALEKAAKAGGKIELEIYDAQNDQSTQNDQIDTMIAKGVDLLVVNLVDRTAAQTIIDKAKAANIPVIFFNREPSRedlk 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 133 RNDDLYLtnIGSDF----LHQGELAVE-WLEDQTSDS------EYVNilhLQGTYGATAQLMRTKA-IEDAESTHSNWKI 200
Cdd:cd01539    99 SYDKAYY--VGTDAeesgIMQGEIIADyWKANPEIDKngdgkiQYVM---LKGEPGHQDAIARTKYsVKTLNDAGIKTEQ 173
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 201 VAQLYGDFTEAKGYEVMTEYLKKNKD-IDVLYSENDNMTFGAMRALDEAG-ITYGENGQVKIITFDATKTALQYCLDGKI 278
Cdd:cd01539   174 LAEDTANWDRAQAKDKMDAWLSKYGDkIELVIANNDDMALGAIEALKAAGyNTGDGDKYIPVFGVDATPEALEAIKEGKM 253

                  .
gi 1079631681 279 S 279
Cdd:cd01539   254 L 254
PBP1_ABC_sugar_binding-like cd19972
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
40-307 2.98e-22

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380627 [Multi-domain]  Cd Length: 269  Bit Score: 94.04  E-value: 2.98e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIANTKSMsQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd19972     1 TIGLAVANLQADFFNQIKQSV-EAEAKKKGYKVITVDAKGDSATQVNQIQDLITQNIDALIYIPAGATAAAVPVKAARAA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDDLYltnIGSDFLHQGELAVEWLEDQTSDSEYVNILHlqGTYGATAQLMRTKAIEDAESTHSNWK 199
Cdd:cd19972    80 GIPVIAVDRNPEDAPGDTF---IATDSVAAAKELGEWVIKQTGGKGEIAILH--GQLGTTPEVDRTKGFQEALAEAPGIK 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 200 IVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCLDGKIS 279
Cdd:cd19972   155 VVAEQTADWDQDEGFKVAQDMLQANPNITVFFGQSDAMALGAAQAVKVAGL----DHKIWVVGFDGDVAGLKAVKDGVLD 230
                         250       260
                  ....*....|....*....|....*....
gi 1079631681 280 L-CVECNPMHGPLVEQLIKRYRSGETIPK 307
Cdd:cd19972   231 AtMTQQTQKMGRLAVDSAIDLLNGKAVPK 259
PBP1_TmRBP-like cd19967
D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ...
69-283 3.41e-22

D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ribose binding protein (ttRBP); Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.


Pssm-ID: 380622 [Multi-domain]  Cd Length: 272  Bit Score: 93.93  E-value: 3.41e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVrnDDLYLTNIGSDFLH 148
Cdd:cd19967    29 GYEVTVFDHQNDTAKEAELFDTAIASGAKAIILDPADADASIAAVKKAKDAGIPVFLIDREINA--EGVAVAQIVSDNYQ 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 149 QG-ELAVEWLEDQTSDSEYVNILhlqGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDI 227
Cdd:cd19967   107 GAvLLAQYFVKLMGEKGLYVELL---GKESDTNAQLRSQGFHSVIDQYPELKMVAQQSADWDRTEAFEKMESILQANPDI 183
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1079631681 228 DVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVE 283
Cdd:cd19967   184 KGVICGNDEMALGAIAALKAAGRA----GDVIIVGFDGSNDVRDAIKEGKISATVL 235
PBP1_TorT-like cd06306
TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor ...
79-310 6.94e-22

TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria; TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type 1 periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.


Pssm-ID: 380529 [Multi-domain]  Cd Length: 269  Bit Score: 93.03  E-value: 6.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  79 QQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPViiIDRSVAVRNDDLyLTNIGSDFLHQGELAVEWLE 158
Cdd:cd06306    41 TNLSKQISQLEDCVASGADAILLGAISFDGLDPKVAEAAAAGIPV--IDLVNGIDSPKV-AARVLVDFYDMGYLAGEYLV 117
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 159 DQtSDSEYVNILHLQGTYGATAQLMRTKAIEDAeSTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSeNDNMT 238
Cdd:cd06306   118 EH-HPGKPVKVAWFPGPAGAGWAEDREKGFKEA-LAGSNVEIVATKYGDTGKAVQLNLVEDALQAHPDIDYIVG-NAVAA 194
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1079631681 239 FGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVEQLIKRYRSGETIPKHVF 310
Cdd:cd06306   195 EAAVGALREAGLT----GKVKVVSTYLTPGVYRGIKRGKILAAPSDQPvLQGRIAVDQAVRALEGKPVPKHVG 263
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
66-264 1.68e-21

ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily; Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.


Pssm-ID: 380491 [Multi-domain]  Cd Length: 264  Bit Score: 91.81  E-value: 1.68e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEgwDMILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSD 145
Cdd:cd06267    26 RERGYSLLLCNTDEDPEREREYLRLLLSRRVDGIILAPSSLD--DELLEELLAAGIPVVLIDRRL----DGLGVDSVVVD 99
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLedqtSDSEYVNILHLQGTYGATAQLMRT----KAIEDAESTHSNWKIVaqlYGDFTEAKGYEVMTEYL 221
Cdd:cd06267   100 NYAGAYLATEHL----IELGHRRIAFIGGPLDLSTSRERLegyrDALAEAGLPVDPELVV---EGDFSEESGYEAARELL 172
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1079631681 222 KKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06267   173 ALPPRPTAIFAANDLMAIGALRALRELGLRVPE--DISVVGFD 213
PBP1_tmGBP cd06314
periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and ...
67-286 1.49e-20

periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs; Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are members of the type 1 periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).


Pssm-ID: 380537 [Multi-domain]  Cd Length: 271  Bit Score: 89.56  E-value: 1.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELI------IENAKQQQdnqfaAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLT 140
Cdd:cd06314    27 ELGVNVEfvgpqkSDAAEQVQ-----LIEDLIARGVDGIAISPNDPEAVTPVINKAADKGIPVITFDSDA---PDSKRLA 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 141 NIGSDFLHQGELAVEWLEDQTSDSEYVNILhlQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEY 220
Cdd:cd06314    99 YIGTDNYEAGREAGELMKKALPGGGKVAII--TGGLGADNLNERIQGFKDALKGSPGIEIVDPLSDNDDIAKAVQNVEDI 176
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1079631681 221 LKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNP 286
Cdd:cd06314   177 LKANPDLDAIFGVGAYNGPAIAAALKDAGKV----GKVKIVGFDTLPETLQGIKDGVIAATVGQRP 238
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
69-279 1.80e-20

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380547 [Multi-domain]  Cd Length: 317  Bit Score: 89.97  E-value: 1.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFI--LEGVDLIVIAPTIEEGWDMiLNEVQSAGIPVIIIDRSVAVRNDDLYLTN----- 141
Cdd:cd06324    30 GIELEVLYANRNRFKMLELAEELLarPPKPDYLILVNEKGVAPEL-LELAEQAKIPVFLINNDLTDEERALLGKPrekfk 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 142 --IGS---DFLHQG-ELAVEWLED--QTSDSEYVNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKG 213
Cdd:cd06324   109 ywLGSivpDNEQAGyLLAKALIKAarKKSDDGKIRVLAISGDKSTPASILREQGLRDALAEHPDVTLLQIVYANWSEDEA 188
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1079631681 214 YEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFDATKTALQYCLDGKIS 279
Cdd:cd06324   189 YQKTEKLLQRYPDIDIVWAANDAMALGAIDALEEAGLKPGKD--VLVGGIDWSPEALQAVKDGELT 252
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
84-312 1.10e-19

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380659 [Multi-domain]  Cd Length: 273  Bit Score: 86.90  E-value: 1.10e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  84 QFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQTSD 163
Cdd:cd20004    46 QIQIIEYFIDQGVDGIVLAPLDRKALVAPVERARAQGIPVVIIDSDL---GGDAVISFVATDNYAAGRLAAKRMAKLLNG 122
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 164 SEYVNILHLQGTYGATAQlmRTKA-IEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAM 242
Cdd:cd20004   123 KGKVALLRLAKGSASTTD--RERGfLEALKKLAPGLKVVDDQYAGGTVGEARSSAENLLNQYPDVDGIFTPNESTTIGAL 200
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079631681 243 RALDEAgityGENGQVKIITFDATKTALQYCLDGKISLCVECNPMH-GPL-VEQLIKRYRsGETIPKHVFID 312
Cdd:cd20004   201 RALRRL----GLAGKVKFIGFDASDLLLDALRAGEISALVVQDPYRmGYLgVKTAVAALR-GKPVPKRIDTG 267
PBP1_LacI-like cd06290
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
68-264 3.94e-19

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380513 [Multi-domain]  Cd Length: 267  Bit Score: 85.36  E-value: 3.94e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVI-APTIEEgwdmILNEVqSAGIPVIIIDRSVavrnDDLYLTNIGSD 145
Cdd:cd06290    28 SGYTLIVSTSHWNADRELEILRLLLARKVDgIIVVgGFGDEE----LLKLL-AEGIPVVLVDREL----EGLNLPVVNVD 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMR----TKAIEDAESTHSNWKIVaqlYGDFTEAKGYEVMTEYL 221
Cdd:cd06290    99 NEQGGYNATNHLIDLG----HRRIVHISGPEDHPDAQERyagyRRALEDAGLEVDPRLIV---EGDFTEESGYEAMKKLL 171
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1079631681 222 KKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06290   172 KRGGPFTAIFAANDLMALGAMKALREAGIRVPD--DVSVIGFD 212
PBP1_ABC_sugar_binding-like cd06317
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
67-323 4.51e-19

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380540 [Multi-domain]  Cd Length: 281  Bit Score: 85.51  E-value: 4.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDrsvAVRNDDLYLTNIGSDF 146
Cdd:cd06317    27 DLGVDLVVFNANDDPSKQNTAVDNYIARGVDAIILDAIDVNGSIPAIKRASEAGIPVIAYD---AVIPSDFQAAQVGVDN 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQ----GELAVEWLEDQTSDSEYVnilhlqGTYGATAQL---MRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTE 219
Cdd:cd06317   104 LEGgkeiGKYAADYIKAELGGQAKI------GVVGALSSLiqnQRQKGFEEALKANPGVEIVATVDGQNVQEKALSAAEN 177
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 220 YLKKNKDIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLD-GKISLCVECNP--MHGPLVEQLI 296
Cdd:cd06317   178 LLTANPDLDAIYATGEPALLGAVAAVRSQGRQ----GKIKVFGWDLTKQAIFLGIDeGVLQAVVQQDPekMGYEAVKAAV 253
                         250       260
                  ....*....|....*....|....*..
gi 1079631681 297 KrYRSGETIPKHVFIDEAAFTREDLTQ 323
Cdd:cd06317   254 K-AIKGEDVEKTIDVPPTIVTKENVDQ 279
PBP1_ABC_xylose_binding-like cd19992
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
40-282 9.35e-19

periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380647 [Multi-domain]  Cd Length: 284  Bit Score: 84.56  E-value: 9.35e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSqLGSESDWRIANTKSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSA 119
Cdd:cd19992     1 KIGVS-FPTQQEERWQKDKEYMEEEAKELGVELIFQVADNDAKTQASQVENLLAQGIDVLIIAPVDAGAAANIVDKAKAA 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 120 GIPVIIIDRSVAVRNDDLYltnIGSDFLHQGELAVEWLEDQTSDSEYVNILHLQGTygATAQLMRT---KAIEDAESThS 196
Cdd:cd19992    80 GVPVISYDRLILNADVDLY---VGRDNYKVGQLQAEYALEAVPKGNYVILSGDPGD--NNAQLITAgamDVLQPAIDS-G 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 197 NWKIVAQLYGD-FTEAKGYEVMTEYLKKNK-DIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCL 274
Cdd:cd19992   154 DIKIVLDQYVKgWSPDEAMKLVENALTANNnNIDAVLAPNDGMAGGAIQALKAQGL----AGKVFVTGQDAELAALKRIV 229

                  ....*...
gi 1079631681 275 DGKISLCV 282
Cdd:cd19992   230 EGTQTMTV 237
PBP1_ABC_sugar_binding-like cd06300
periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are ...
40-260 1.09e-18

periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380523 [Multi-domain]  Cd Length: 302  Bit Score: 84.68  E-value: 1.09e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRIAntksMSQTFTND-NGY-------ELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDM 111
Cdd:cd06300     1 TIGLSNTYAGNSWREQ----MIASLKADaAQSgqkglvkELIVANSNGDATEQIAQIRNLIDQGVDAIIINPSSPTALNA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 112 ILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDA 191
Cdd:cd06300    77 VIEQAADAGIPVVAFDGAV----TSPDAYNVSNDQVEWGRLGAKWLFEALGGKG--NVLVVRGIAGAPASADRHAGVKEA 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 192 ESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTfGAMRALDEAG------ITYGENGQVKI 260
Cdd:cd06300   151 LAEYPGIKVVGEVFGGWDEATAQTAMLDFLATHPQVDGVWTQGGEDT-GVLQAFQQAGrppvpiVGGDENGFAKQ 224
PRK10653 PRK10653
ribose ABC transporter substrate-binding protein RbsB;
58-312 1.89e-18

ribose ABC transporter substrate-binding protein RbsB;


Pssm-ID: 182620 [Multi-domain]  Cd Length: 295  Bit Score: 83.99  E-value: 1.89e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  58 KSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEegwDMILNEVQSA---GIPVIIIDRsVAVRN 134
Cdd:PRK10653   45 KDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDS---DAVGNAVKMAnqaNIPVITLDR-GATKG 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 135 DdlYLTNIGSDFLHQGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLYGDFTEAKGY 214
Cdd:PRK10653  121 E--VVSHIASDNVAGGKMAGDFIAKKLGEG--AKVIQLEGIAGTSAARERGEGFKQAVAAH-KFNVLASQPADFDRTKGL 195
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 215 EVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygengQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPLVE 293
Cdd:PRK10653  196 NVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKS-----DVMVVGFDGTPDGIKAVNRGKLAATIAQQPdQIGAIGV 270
                         250
                  ....*....|....*....
gi 1079631681 294 QLIKRYRSGETIPKHVFID 312
Cdd:PRK10653  271 ETADKVLKGEKVEAKIPVD 289
PBP1_ABC_sugar_binding-like cd06311
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
75-251 2.87e-18

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380534 [Multi-domain]  Cd Length: 270  Bit Score: 83.18  E-value: 2.87e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  75 ENAKQQQDnqfaAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYltnIGSDFLHQGELAV 154
Cdd:cd06311    39 SNANEQVS----QLEDLIAQKVDAIVILPQDSEELTVAAQKAKDAGIPVVNFDRGLNVLIYDLY---VAGDNPGMGVVSA 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 155 EWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSEN 234
Cdd:cd06311   112 EYIGKKLGGKG--NVVVLEVPSSGSVNEERVAGFKEVIKGNPGIKILAMQAGDWTREDGLKVAQDILTKNKKIDAVWAAD 189
                         170
                  ....*....|....*..
gi 1079631681 235 DNMTFGAMRALDEAGIT 251
Cdd:cd06311   190 DDMAIGVLQAIKEAGRT 206
PBP1_ABC_sugar_binding-like cd20007
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
69-317 3.03e-17

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380662 [Multi-domain]  Cd Length: 271  Bit Score: 80.36  E-value: 3.03e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQ-QQDNQFAAIRRFILEGVDLIVIAPTIEEGwdMI--LNEVQSAGIPVIIIDRSVAvrNDDLYLTNIGSD 145
Cdd:cd20007    29 GVELDVQGPPTfDPTLQTPIVNAVIAKKPDALLIAPTDPQA--LIapLKRAADAGIKVVTVDTTLG--DPSFVLSQIASD 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQTSDSEYVniLHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNK 225
Cdd:cd20007   105 NVAGGALAAEALAELIGGKGKV--LVINSTPGVSTTDARVKGFAEEMKKYPGIKVLGVQYSENDPAKAASIVAAALQANP 182
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 226 DIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNPMH-GPL-VEQLIKrYRSGE 303
Cdd:cd20007   183 DLAGIFGTNTFSAEGAAAALRNAGKT----GKVKVVGFDASPAQVEQLKAGTIDALIAQKPAEiGYLaVEQAVA-ALTGK 257
                         250
                  ....*....|....
gi 1079631681 304 TIPKHVFIDEAAFT 317
Cdd:cd20007   258 PVPKDILTPFVVIT 271
PBP1_ABC_sugar_binding-like cd19998
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
51-256 7.48e-17

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380653 [Multi-domain]  Cd Length: 302  Bit Score: 79.64  E-value: 7.48e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  51 DWRI--ANT-KSMSQTFTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIID 127
Cdd:cd19998    12 DWRQemINIaKAAAKQPPYADKVELKVVSSGTDVQAQISAIDNMIAAGYDAILIYAISPTALNPVIKRACDAGIVVVAFD 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 128 rSVaVRNDDLYltNIGSDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGD 207
Cdd:cd19998    92 -NV-VDEPCAY--NVNTDQAKAGEQTAQWLVDKLGGKG--NILMVRGVPGTSVDRDRYEGAKEVFKKYPDIKVVAEYYGN 165
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 208 FTEAKGYEVMTEYLKKNKDIDVLYSENDnmTFGAMRALDEAGI------TYGENG 256
Cdd:cd19998   166 WDDGTAQKAVADALAAHPDVDGVWTQGG--ETGVIKALQAAGHplvpvgGEAENG 218
PBP1_ABC_sugar_binding-like cd19997
monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic ...
40-257 2.32e-15

monosaccharide ABC transporter substrate binding protein such as CUT2; Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.


Pssm-ID: 380652 [Multi-domain]  Cd Length: 305  Bit Score: 75.40  E-value: 2.32e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  40 VIGFSQLGSESDWRiantKSMSQTFTN------DNGY--ELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDM 111
Cdd:cd19997     1 VIALSNSYAGNTWR----QQMVDAFEEaakkakADGLiaDYIVVNADGSATTQISQIQNLILQGVDAIVIDAASPTALNG 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 112 ILNEVQSAGIPVIIIDrsVAVRNDDLYLTNIgsDFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQLMRTKAIEDA 191
Cdd:cd19997    77 AIQQACDAGIKVVVFD--SGVTEPCAYILNN--DFEDYGAASVEYVADRLGGKG--NVLEVRGVAGTSPDEEIYAGQVEA 150
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 192 ESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNmTFGAMRALDEAG----ITYGENGQ 257
Cdd:cd19997   151 LKKYPDLKVVAEVYGNWTQSVAQKAVTGILPSLPEVDAVITQGGD-GYGAAQAFEAAGrplpIIIGGNRG 219
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
67-264 3.78e-15

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380544 [Multi-domain]  Cd Length: 270  Bit Score: 74.25  E-value: 3.78e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDrsVAVRNDDlylTNIGSDF 146
Cdd:cd06321    29 NPGAKVTVVDARYDLAKQFSQIDDFIAQGVDLILLNAADSAGIEPAIKRAKDAGIIVVAVD--VAAEGAD---ATVTTDN 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTSDSEYVNILhlQGTYgATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKD 226
Cdd:cd06321   104 VQAGYLACEYLVEQLGGKGKVAII--DGPP-VSAVIDRVNGCKEALAEYPGIKLVDDQNGKGSRAGGLSVMTRMLTAHPD 180
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1079631681 227 IDVLYSENDNMTFGAMRALDEAGitygeNGQVKIITFD 264
Cdd:cd06321   181 VDGVFAINDPGAIGALLAAQQAG-----RDDIVITSVD 213
PBP1_ABC_sugar_binding-like cd20005
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
75-287 6.04e-15

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380660 [Multi-domain]  Cd Length: 274  Bit Score: 73.82  E-value: 6.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  75 ENAKQQQDNQFAAIrrfILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAV 154
Cdd:cd20005    40 ESDVDKQIEMLDNA---IAKKPDAIALAALDTNALLPQLEKAKEKGIPVVTFDSGV---PSDLPLATVATDNYAAGALAA 113
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 155 EWLEDQTSDS-EYVNILHLQGTygATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSE 233
Cdd:cd20005   114 DHLAELIGGKgKVAIVAHDATS--ETGIDRRDGFKDEIKEKYPDIKVVNVQYGVGDHAKAADIAKAILQANPDLKGIYAT 191
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 234 NDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNPM 287
Cdd:cd20005   192 NEGAAIGVANALKEMGKL----GKIKVVGFDSGEAQIDAIKNGVIAGSVTQNPY 241
PBP1_GalS-like cd06270
ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory ...
67-311 6.43e-15

ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380494 [Multi-domain]  Cd Length: 266  Bit Score: 73.32  E-value: 6.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEegwDMILNEVQSAGIPVIIIDRSVA-VRNDDLYLTNIGS 144
Cdd:cd06270    27 AHGKQLLITSGHHDAEEEREAIEFLLDRRCDaIILHSRALS---DEELILIAEKIPPLVVINRYIPgLADRCVWLDNEQG 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 dflhqGELAVEWLEDQ--------TSDSE-YVNILHLQGtYgataqlmrTKAIEDAESTHSNWKIVaqlYGDFTEAKGYE 215
Cdd:cd06270   104 -----GRLAAEHLLDLghrriaciTGPLDiPDARERLAG-Y--------RDALAEAGIPLDPSLII---EGDFTIEGGYA 166
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 216 VMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTAlQYcldgkislcveCNP----MHGPL 291
Cdd:cd06270   167 AAKQLLARGLPFTALFAYNDDMAIGALAALHEAGIKVPE--DVSVIGFDDVPLA-RY-----------LSPklttVHYPI 232
                         250       260
                  ....*....|....*....|....*..
gi 1079631681 292 -------VEQLIKRYRSGETIPKHVFI 311
Cdd:cd06270   233 eemaqaaAELALNLAYGEPLPISHEFT 259
PBP1_ABC_xylose_binding-like cd19995
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
71-282 1.23e-14

periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380650 [Multi-domain]  Cd Length: 294  Bit Score: 73.09  E-value: 1.23e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  71 ELIIENAK---QQQDNQF-AAIRRfileGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLT----NI 142
Cdd:cd19995    34 KVIYQNANgdaSTQQQQAeAAITQ----GAKVLVVDPVDSNAAAGIVAKAAQAGVPVIAYDRLILGGPADYYVSfdnvAV 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 143 GsdfLHQGELAVEWLEDQTSDSeyVNILHL---QGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYG-DFTEAKGYEVMT 218
Cdd:cd19995   110 G---EAQAQSLVDHLKAIGKKG--VNIVMIngsPTDNNAGLFKKGAHEVLDPLGDSGELKLVCEYDTpDWDPANAQTAME 184
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 219 EYLKKN-KDIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCLDGKISLCV 282
Cdd:cd19995   185 QALTKLgNNIDGVLSANDGLAGGAIAALKAQGL----AGKVPVTGQDATVAGLQRILAGDQYMTV 245
PBP1_ABC_xylose_binding-like cd01538
periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong ...
69-276 4.01e-14

periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380480 [Multi-domain]  Cd Length: 283  Bit Score: 71.30  E-value: 4.01e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTnigSDFLH 148
Cdd:cd01538    29 GAKVLVQSADGDKAKQASQIENLLTQGADVLVLAPVDGQALSPVVAEAKAEGIKVIAYDRLILNADVDYYIS---FDNEK 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 149 QGELAVEWLEDQTSDSEYVNI----------LHLQGTYgataqlmrtKAIEDAESThSNWKIVA-QLYGDFTEAKGYEVM 217
Cdd:cd01538   106 VGELQAQALLDAKPEGNYVLIggsptdnnakLFRDGQM---------KVLQPAIDS-GKIKVVGdQWVDDWLPANAQQIM 175
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 218 TEYLKKNK-DIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCLDG 276
Cdd:cd01538   176 ENALTANGnNVDAVVASNDGTAGGAIAALKAQGL----SGGVPVSGQDADLAAIKRILAG 231
PBP1_ABC_xylose_binding cd19991
D-xylose binding periplasmic protein; Periplasmic xylose-binding component of the ABC-type ...
69-282 4.79e-14

D-xylose binding periplasmic protein; Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380646 [Multi-domain]  Cd Length: 284  Bit Score: 71.11  E-value: 4.79e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTnigSDFLH 148
Cdd:cd19991    29 GAEVIVQSANGDDEKQISQAEELIEQGVDVLVVVPNNGEALAPIVKEAKKAGVPVLAYDRLILNADVDLYVS---FDNEK 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 149 QGELAVEWLEDQTSDSEYVNIlhlqgtYGAT----AQLMRtKAIEDAESTHSN---WKIVAQLY-GDFTEAKGYEVMTEY 220
Cdd:cd19991   106 VGELQAEALVKAKPKGNYVLL------GGSPtdnnAKLFR-EGQMKVLQPLIDsgdIKVVGDQWvDDWDPEEALKIMENA 178
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1079631681 221 LKKNK-DIDVLYSENDNMTFGAMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCV 282
Cdd:cd19991   179 LTANNnKIDAVIASNDGTAGGAIQALAEQGLA----GKVAVSGQDADLAACQRIVEGTQTMTI 237
PBP1_MalR-like cd06294
ligand-binding domain of maltose transcription regulator MalR which is a member of the ...
66-266 9.12e-14

ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors; This group includes the ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380517 [Multi-domain]  Cd Length: 269  Bit Score: 70.30  E-value: 9.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDnQFAAIRRFILEG-VD-LIVIAPTIEegwDMILNEVQSAGIPVIIIDRSVAvRNDDLYLTNig 143
Cdd:cd06294    31 NENGYSLLLATGNTEEE-LLEEVKRMVRGRrVDgFILLYSKED---DPLIEYLKEEGFPFVVIGKPLD-DNDVLYVDN-- 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 sDFLHQGELAVEWLEDQTSDseyvNILHLQGTYGATAQLMRT----KAIEDAESTHSNWKIvaqLYGDFTEAKGYEVMTE 219
Cdd:cd06294   104 -DNVQAGYEATEYLIDKGHK----RIAFIGGDKNLVVSIDRLqgykQALKEAGLPLDDDYI---LLLDFSEEDGYDALQE 175
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 220 YLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDAT 266
Cdd:cd06294   176 LLSKPPPPTAIVATDDLLALGVLRYLQELGLRVPE--DVSIISFNNS 220
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
84-271 2.20e-13

monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380663 [Multi-domain]  Cd Length: 277  Bit Score: 69.18  E-value: 2.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  84 QFAAIRRFILEGVDLIVIAPTIEegwDMI--LNEVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLHQGELAVEWLEDQ- 160
Cdd:cd20008    46 QVNLVENAISRKPDAIVLAPNDT---AALvpAVEAADAGIPVVLVDSGA---NTDDYDAFLATDNVAAGALAADELAELl 119
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 161 -TSDSEYVNILHLQGTYGATAQLMRTKAIEDAESTHSNW-KIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMT 238
Cdd:cd20008   120 kASGGGKGKVAIISFQAGSQTLVDREEGFRDYIKEKYPDiEIVDVQYSDGDIAKALNQTTDLLTANPDLVGIFGANNPSA 199
                         170       180       190
                  ....*....|....*....|....*....|...
gi 1079631681 239 FGAMRALDEAGITygenGQVKIITFDATKTALQ 271
Cdd:cd20008   200 VGVAQALAEAGKA----GKIVLVGFDSSPDEVA 228
PBP1_EndR-like cd19977
periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its ...
68-264 4.13e-13

periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its close homologs; This group includes the ligand-binding domain of putative repressor of the endoglucanase operon from Paenibacillus polymyxa and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380632 [Multi-domain]  Cd Length: 264  Bit Score: 68.33  E-value: 4.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELII----ENAKQQQDnqfaAIRRFILEGVDLIVIAPTieEGWDMILNEVQSAGIPVIIIDRSVavrnDDLYLTNIG 143
Cdd:cd19977    28 NGYHVILcntdEDPEKEKK----YIEMLRAKQVDGIIIAPT--GGNEDLIEKLVKSGIPVVFVDRYI----PGLDVDTVV 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 SDFLHQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKK 223
Cdd:cd19977    98 VDNFKGAYQATEHLIELG----HKRIAFITYPLELSTRQERLEGYKAALADHGLPVDEELIKHVDRQDDVRKAISELLKL 173
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1079631681 224 NKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd19977   174 EKPPDAIFAANNLITLEVLKAIKELGLRIPD--DIALIGFD 212
PBP1_Qymf-like cd06291
ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing ...
68-269 1.17e-12

ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs; This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380514 [Multi-domain]  Cd Length: 264  Bit Score: 66.77  E-value: 1.17e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEegwdmILNEVQSAGIPVIIIDRSVavrNDDLYLtnIGSDFL 147
Cdd:cd06291    28 KGYKMILCNSNEDEEKEKEYLEMLKRNKVDGIILGSHSL-----DIEEYKKLNIPIVSIDRYL---SEGIPS--VSSDNY 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 148 HQGELAVEWLEDQTSDseyvNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLYG--DFTEAKGYEVMTEYLKKNK 225
Cdd:cd06291    98 QGGRLAAEHLIEKGCK----KILHIGGPSNNSPANERYRGFEDALKEA-GIEYEIIEIDenDFSEEDAYELAKELLEKYP 172
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1079631681 226 DIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTA 269
Cdd:cd06291   173 DIDGIFASNDLLAIGVLKALQKLGIRVPE--DVQIIGFDGIEIS 214
PBP1_LacI-like cd06280
ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus ...
67-264 3.87e-12

ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380503 [Multi-domain]  Cd Length: 266  Bit Score: 65.36  E-value: 3.87e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTieEGWDMILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSDF 146
Cdd:cd06280    27 KHGYQVILANTDEDPEKEKRYLDSLLSKQVDGIILAPS--AGPSRELKRLLKHGIPIVLIDREV----EGLELDLVAGDN 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQL--YGDFTEAKGYEVMTEYLKKN 224
Cdd:cd06280   101 REGAYKAVKHLIELG----HRRIGLITGPLEISTTRERLAGYREALAEA-GIPVDESLifEGDSTIEGGYEAVKALLDLP 175
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1079631681 225 KDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06280   176 PRPTAIFATNNLMAVGALRALRERGLEIPQ--DISVVGFD 213
PBP1_LacI-like cd06299
ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum ...
69-264 4.95e-12

ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia; This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380522 [Multi-domain]  Cd Length: 268  Bit Score: 64.99  E-value: 4.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIE--EGWDMILNevqsAGIPVIIIDRSVAVRNDdlyLTNIGSDF 146
Cdd:cd06299    29 GYSVILGNSDEDPEREDESLEMLLSQRVDGIIAVPTGEnsEGLQALIA----QGLPVVFVDREVEGLGG---VPVVTSDN 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTSDSeyvnILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLY--GDFTEAKGYEVMTEYLKKN 224
Cdd:cd06299   102 RPGAREAVEYLVSLGHRR----IGYISGPLSTSTGRERLAAFRAALTAA-GIPIDEELVafGDFRQDSGAAAAHRLLSRG 176
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1079631681 225 KDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFD 264
Cdd:cd06299   177 DPPTALIAGDSLMALGAIQALRELGLRIGDD--VSLISFD 214
PBP1_ChvE cd19994
periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling ...
67-282 6.39e-12

periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling system; Periplasmic aldose-monosaccharides binding protein ChvE that belongs to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380649 [Multi-domain]  Cd Length: 304  Bit Score: 65.34  E-value: 6.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSvaVRNDDLYLTNIGSDF 146
Cdd:cd19994    27 EAGYTVDLQYADDDVATQNSQIENMINKGAKVLVIAPVDGSALGDVLEEAKDAGIPVIAYDRL--IMNTDAVDYYVTFDN 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQT---SDSEYVNILHLQGTYG-ATAQLMRTKA-------IED----AESTHSNWKIVAQLYGDFTEA 211
Cdd:cd19994   105 EKVGELQGQYLVDKLglkDGKGPFNIELFAGSPDdNNAQLFFKGAmevlqpyIDDgtlvVRSGQTTFEQVATPDWDTETA 184
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 212 KGY--EVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITygeNGQVKIIT-FDATKTALQYCLDGKISLCV 282
Cdd:cd19994   185 QARmeTLLSAYYTGGKKLDAVLSPNDGIARGVIEALKAAGYD---TGPWPVVTgQDAEDASVKSILDGEQSMTV 255
PBP1_ABC_sugar_binding-like cd06312
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
88-282 6.67e-12

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380535 [Multi-domain]  Cd Length: 272  Bit Score: 64.95  E-value: 6.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  88 IRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDL-YLTNIGSDFLHQGELAVEWLEDQTSDSeY 166
Cdd:cd06312    50 IEQAIAAKPDGIIVTIPDPDALEPALKRAVAAGIPVIAINSGDDRSKERLgALTYVGQDEYLAGQAAGERALEAGPKN-A 128
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 167 VNILHLQGtygATAQLMRTKAIEDAESTHSnwKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALD 246
Cdd:cd06312   129 LCVNHEPG---NPGLEARCKGFADAFKGAG--ILVELLDVGGDPTEAQEAIKAYLQADPDTDAVLTLGPVGADPALKAVK 203
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1079631681 247 EAGitygENGQVKIITFDATKTALQYCLDGKISLCV 282
Cdd:cd06312   204 EAG----LKGKVKIGTFDLSPETLEAIKDGKILFAI 235
PBP1_ABC_sugar_binding-like cd19969
monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of ...
83-279 1.07e-11

monosaccharide ABC transporter substrate binding protein; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380624 [Multi-domain]  Cd Length: 278  Bit Score: 64.28  E-value: 1.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  83 NQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYltnIGSDFLHQGELAVEWLEDQTS 162
Cdd:cd19969    44 EQITAIEQAIAKNPDGIAVSAIDPEALTPTINKAVDAGIPVVTFDSDAPESKRISY---VGTDNYEAGYAAAEKLAELLG 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 163 DSEYVNILHLQGTYGATAqlmRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAM 242
Cdd:cd19969   121 GKGKVAVLTGPGQPNHEE---RVEGFKEAFAEYPGIEVVAVGDDNDDPEKAAQNTSALLQAHPDLVGIFGVDASGGVGAA 197
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1079631681 243 RALDEAGITygenGQVKIITFDATKTALQYCLDGKIS 279
Cdd:cd19969   198 QAVREAGKT----GKVKIVAFDDDPETLDLIKDGVID 230
PBP1_repressor_sugar_binding-like cd01537
Ligand-binding domain of the LacI-GalR family of transcription regulators and the ...
69-272 2.61e-11

Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems; Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor.


Pssm-ID: 380479 [Multi-domain]  Cd Length: 265  Bit Score: 63.03  E-value: 2.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEEgwDMILNEVQSAGIPVIIIDRSVAvRNDDLYltNIGSDFL 147
Cdd:cd01537    29 GVQLLMNDSQNDQEKQNDQIDVLLAKRVKgLAINLVDPAA--AGVAEKARGQNVPVVFFDKEPS-RYDKAY--YVITDSK 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 148 HQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMRT----KAIEDAESTHSNWKIVAqlyGDFTEAKGYEVMTEYLKK 223
Cdd:cd01537   104 EGGIIQGDLLAKHG----HIQIVLLKGPLGHPDAEARLagviKELNDKGIKTEQLQLDT---GDWDTASGKDKMDQWLSG 176
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1079631681 224 NKDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFDATKTALQY 272
Cdd:cd01537   177 PNKPTAVIANNDAMAMGAVEALKEHGLRVPSD--ISVFGYDALPEALKS 223
PBP1_DegA_Like cd19976
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
66-264 2.82e-11

ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380631 [Multi-domain]  Cd Length: 268  Bit Score: 63.04  E-value: 2.82e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMIlNEVQSAGIPVIIIDRSVAVRNDDlyltNIGSD 145
Cdd:cd19976    26 NELGYNIILCNTYNDFEREKKYIQELKERNVDGIIIASSNISDEAII-KLLKEEKIPVVVLDRYIEDNDSD----SVGVD 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQ--------TSDSEYVNILH-LQGtYgataqlmrTKAIEDAEST-HSNWkivaqLYGDFTEAKGYE 215
Cdd:cd19976   101 DYRGGYEATKYLIELghtrigciVGPPSTYNEHErIEG-Y--------KNALQDHNLPiDESW-----IYSGESSLEGGY 166
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1079631681 216 VMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFD 264
Cdd:cd19976   167 KAAEELLKSKNPTAIFAGNDLIAMGVYRAALELGLKIPED--LSVIGFD 213
XylF COG4213
ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism] ...
69-282 3.43e-11

ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 443359 [Multi-domain]  Cd Length: 310  Bit Score: 63.23  E-value: 3.43e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRsvAVRND--DLYLTnigSDF 146
Cdd:COG4213    32 GYEVDVQNANGDVATQLSQIENMITKGADVLVIAPIDGTALAAVLEKAKAAGIPVIAYDR--LILNSdvDYYVS---FDN 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTSDSEYVNILHLQGtyGAT---AQLMRTKA-------IEDAEsthsnWKIVaqlYGDFTE----AK 212
Cdd:COG4213   107 VKVGELQGQYLVDGLPLKGKGNIELFGG--SPTdnnATLFFEGAmsvlqpyIDSGK-----LVVV---SGQWTLgwdpET 176
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1079631681 213 GYEVMTEYLKKN-KDIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCLDGKISLCV 282
Cdd:COG4213   177 AQKRMENLLTANgNKVDAVLAPNDGLAGGIIQALKAQGL----AGKVVVTGQDAELAAVQRILAGTQYMTV 243
PBP1_LacI-like cd06278
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
69-264 5.41e-11

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380501 [Multi-domain]  Cd Length: 266  Bit Score: 62.17  E-value: 5.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQfAAIRRFILEGVD-LIVIAPTIEegwDMILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSDFL 147
Cdd:cd06278    29 GLRPLLFNVDDEDDVD-DALRQLLQYRVDgVIVTSATLS---SELAEECARRGIPVVLFNRVV----EDPGVDSVSCDNR 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 148 HQGELAVEWLEDqtsdSEYVNILHLQGTYGATAQLMRTKAIEDAESTHsNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDI 227
Cdd:cd06278   101 AGGRLAADLLLA----AGHRRIAFLGGPEGTSTSRERERGFRAALAEL-GLPPPAVEAGDYSYEGGYEAARRLLAAPDRP 175
                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1079631681 228 DVLYSENDNMTFGAMRAL-DEAGITYGEngQVKIITFD 264
Cdd:cd06278   176 DAIFCANDLMALGALDAArQEGGLVVPE--DISVVGFD 211
PBP1_TreR-like cd01542
ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a ...
58-269 1.14e-10

ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380484 [Multi-domain]  Cd Length: 259  Bit Score: 60.97  E-value: 1.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  58 KSMSQTFtNDNGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEegwDMILNEVQSAGIPVIIIDRSV----AV 132
Cdd:cd01542    19 EGIDEVL-KENGYQPLIANTNLDEEREIEYLETLARQKVDgIILFATEIT---DEHRKALKKLKIPVVVLGQEHegfsCV 94
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 133 RNDDLyltnigsdflHQGELAVEWLEDQTsdseYVNILHLQGTYG--ATAQLmRTKAIEDAESTHSNWKIVAqLYGDFTE 210
Cdd:cd01542    95 YHDDY----------GAGKLLGEYLLKKG----HKNIAYIGVDEEdiAVGVA-RKQGYLDALKEHGIDEVEI-VETDFSM 158
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1079631681 211 AKGYEVMTEYLKKNKdIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTA 269
Cdd:cd01542   159 ESGYEAAKELLKENK-PDAIICATDNIALGAIKALRELGIKIPE--DISVAGFGGYDLS 214
PBP1_ABC_sugar_binding-like cd06316
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
39-264 1.74e-10

periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380539 [Multi-domain]  Cd Length: 294  Bit Score: 60.71  E-value: 1.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  39 YVIGFSQLGSesDWRIANTKSMSQTFtNDNGYELI-IENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQ 117
Cdd:cd06316     2 VAIAMHTTGS--DWSRLQVAGIKDTF-EELGIEVVaVTDANFDPAKQITDLETLIALKPDIIISIPVDPVATAAAYKKVA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 118 SAGIPVIIIDRSVA--VRNDDlYLTNIGSDFLHQGELAVEWLEDQTSDSEYVNILHLQGTYGATAQlmRTKAIEDA-EST 194
Cdd:cd06316    79 DAGIKLVFMDNVPDglEAGKD-YVSVVSSDNRGNGQIAAELLAEAIGGKGKVGIIYHDADFYATNQ--RDKAFKDTlKEK 155
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 195 HSNWKIVAqLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGitygeNGQVKIITFD 264
Cdd:cd06316   156 YPDIKIVA-EQGFADPNDAEEVASAMLTANPDIDGIYVSWDTPALGVISALRAAG-----RSDIKITTVD 219
PBP1_CelR cd06295
ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly ...
66-264 3.43e-10

ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators; This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380518 [Multi-domain]  Cd Length: 273  Bit Score: 59.96  E-value: 3.43e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELII--ENAKQQQDNQFAAIRRfilegVD-LIVIAptieEGWDM-ILNEVQSAGIPVIIIDrsvAVRNDDLYLTn 141
Cdd:cd06295    37 TDRGYDMLLstQDEDANQLARLLDSGR-----ADgLIVLG----QGLDHdALRELAQQGLPMVVWG---APEDGQSYCS- 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 142 IGSDFLHQGELAVEWLEDQ----------TSDSEYvnILHLQGTYGATAQlmrtkaiedaestHS-NWKIVAQLYGDFTE 210
Cdd:cd06295   104 VGSDNVKGGALATEHLIEIgrrriaflgdPPHPEV--ADRLQGYRDALAE-------------AGlEADPSLLLSCDFTE 168
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 211 AKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYgeNGQVKIITFD 264
Cdd:cd06295   169 ESGYAAMRALLDSGTAFDAIFAASDLIAMGAIRALRERGISV--PGDVAVVGYD 220
PBP1_PurR cd06275
ligand-binding domain of purine repressor, PurR, which functions as the master regulatory ...
67-264 5.26e-10

ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli; Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380499 [Multi-domain]  Cd Length: 269  Bit Score: 59.19  E-value: 5.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEEGWDMILNEVQSagIPVIIIDRSVAVRNDDlyltNIGSD 145
Cdd:cd06275    27 RAGYSLILCNSDNDPEKQRAYLDMLAEKRVDgLLLMCSEMTDDDAELLAALRS--IPVVVLDREIAGDNAD----AVLDD 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQ----------TSDSEYVNiLHLQGTYGAtaqlMRTKAIEDAESthsnWKIvaqlYGDFTEAKGYE 215
Cdd:cd06275   101 SFQGGYLATRHLIELghrrigcitgPLEHSVSR-ERLAGFRRA----LAEAGIEVPPS----WIV----EGDFEPEGGYE 167
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1079631681 216 VMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06275   168 AMQRLLSQPPRPTAVFACNDMMALGALRAAQEQGLRVPQ--DISIIGYD 214
PBP1_LacI-like cd06285
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
67-264 6.72e-10

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380508 [Multi-domain]  Cd Length: 269  Bit Score: 58.78  E-value: 6.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTieEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTnigsDF 146
Cdd:cd06285    27 ERGYTVLLADTGDDPERELAALDSLLSRRVDGLIITPA--RDDAPDLQELAARGVPVVLVDRRIGDTALPSVTV----DN 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTSDSeyvnILHLQGTYGATAQLMRTKAIEDAESTHS-NWKIVAQLYGDFTEAKGYEVMTEYLKKNK 225
Cdd:cd06285   101 ELGGRLATRHLLELGHRR----IAVVAGPLNASTGRDRLRGYRRALAEAGlPVPDERIVPGGFTIEAGREAAYRLLSRPE 176
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1079631681 226 DIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06285   177 RPTAVFAANDLMAIGVLRAARDLGLRVPE--DLSVVGFD 213
PBP1_MalI-like cd06289
ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia ...
66-264 6.88e-10

ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria; This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380512 [Multi-domain]  Cd Length: 268  Bit Score: 58.73  E-value: 6.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDmILNEVQSAGIPVIIIDRSVavrnDDLYLTNIGSD 145
Cdd:cd06289    26 EEAGYLVFLANTGEDPERQRRFLRRMLEQGVDGLILSPAAGTTAE-LLRRLKAWGIPVVLALRDV----PGSDLDYVGID 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FLHQGELAVEWLEDQTSDSeyvnILHLQGTYGATAQLMRTKAIEDAESTH-----SNWkIVAqlyGDFTEAKGYEVMTEY 220
Cdd:cd06289   101 NRLGAQLATEHLIALGHRR----IAFLGGLSDSSTRRERLAGFRAALAEAglpldESL-IVP---GPATREAGAEAAREL 172
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1079631681 221 LKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06289   173 LDAAPPPTAVVCFNDLVALGAMLALRRRGLEPGR--DIAVVGFD 214
PBP1_LacI cd01574
ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of ...
67-264 1.35e-09

ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380488 [Multi-domain]  Cd Length: 265  Bit Score: 57.98  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQF-AAIRRFILEGVD-LIVIAPTIeegWDMILNEVQSAGIPVIIIDRSVAVRnddlyLTNIGS 144
Cdd:cd01574    27 ERGYSVSIATVDEDDPASVrEALDRLLSQRVDgIIVIAPDE---AVLEALRRLPPGLPVVIVGSGPSPG-----VPTVSI 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 DFLHQGELAVEWLEDQ--TSdseyvnILHLQGTYGATAQLMRTKAIEDA--ESTHSNWKIVAqlyGDFTEAKGYEVMTEy 220
Cdd:cd01574    99 DQEEGARLATRHLLELghRR------IAHIAGPLDWVDARARLRGWREAleEAGLPPPPVVE---GDWSAASGYRAGRR- 168
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1079631681 221 LKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd01574   169 LLDDGPVTAVFAANDQMALGALRALHERGLRVPE--DVSVVGFD 210
PBP1_GalR cd01544
ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory ...
206-311 4.30e-09

ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism; Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar binding of ABC-type transport systems.


Pssm-ID: 380486 [Multi-domain]  Cd Length: 269  Bit Score: 56.38  E-value: 4.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 206 GDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTAlQYcldgkislcveCN 285
Cdd:cd01544   158 GEFSVESGYEAMKELLKEGDLPTAFFVASDPMAIGALRALQEAGIKVPE--DISIISFNDIEVA-KY-----------VT 223
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1079631681 286 PmhgPL--------------VEQLIKRYRSGETIPKHVFI 311
Cdd:cd01544   224 P---PLttvhipteemgrtaVRLLLERINGGRTIPKKVLL 260
PBP1_CcpA-like cd19975
ligand-binding domain of putative DNA transcription regulators highly similar to that of the ...
66-312 6.80e-09

ligand-binding domain of putative DNA transcription regulators highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation; This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators.


Pssm-ID: 380630 [Multi-domain]  Cd Length: 269  Bit Score: 56.03  E-value: 6.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAP-TIEEGwdmILNEVQSAGIPVIiidrSVAVRNDDLYLTNIGS 144
Cdd:cd19975    26 RENGYSVILCNTGSDEEREKKYLQLLKEKRVDGIIFASgTLTEE---NKQLLKNMNIPVV----LVSTESEDPDIPSVKI 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 DFLHQGELAVEWLEDQTsdseYVNILHLQG-TYGATAQLMRT----KAIEDAEST-HSNWkIVaqlYGDFTEAKGYEVMT 218
Cdd:cd19975    99 DDYQAAYDATNYLIKKG----HRKIAMISGpLDDPNAGYPRYegykKALKDAGLPiKENL-IV---EGDFSFKSGYQAMK 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 219 EYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFDATKTALQYcldgkislcvecNP----MHGPL--- 291
Cdd:cd19975   171 RLLKNKKLPTAVFAASDEMALGVISAAYDHGIRVPED--ISVIGFDNTEIAEMS------------IPplttVSQPFyem 236
                         250       260
                  ....*....|....*....|....*
gi 1079631681 292 ----VEQLIKRYRSGETIPKHVFID 312
Cdd:cd19975   237 gkkaVELLLDLIKNEKKEEKSIVLP 261
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
69-325 6.87e-09

periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily; Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380482 [Multi-domain]  Cd Length: 294  Bit Score: 56.14  E-value: 6.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVaVRNDDLYL--------T 140
Cdd:cd01540    29 GFEVIKIDAKMDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAGIPVIAVDDQL-VDADPMKIvpfvgidaY 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 141 NIGSDflhQGELAVEWLEDQT-SDSEYVNILHL---------QGTYGATAQLMRTKAIEDaesthsnwKIVAQLY-GDFT 209
Cdd:cd01540   108 KIGEA---VGEWLAKEMKKRGwDDVKEVGVLAItmdtlsvcvDRTDGAKDALKAAGFPED--------QIFQAPYkGTDT 176
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 210 EaKGYEVMTEYLKKNKDID--VLYSENDNMTFGAMRALDEAG------ITYGENG-QVKIITFDATKTAlqYCLDGKISl 280
Cdd:cd01540   177 E-GAFNAANAVITAHPEVKhwLVVGCNDEGVLGAVRALEQAGfdaediIGVGIGGyLAADEEFKKQPTG--FKASLYIS- 252
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1079631681 281 cvecNPMHGPL-VEQLIKRYRSGETIPKHVFIDEAAFTREDLTQEM 325
Cdd:cd01540   253 ----PDKHGYIaAEELYNWITDGKPPPAETLTDGVIVTRDNYKEVM 294
PBP1_ABC_sugar_binding-like cd19973
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
68-278 9.20e-09

monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins.


Pssm-ID: 380628 [Multi-domain]  Cd Length: 285  Bit Score: 55.55  E-value: 9.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELIIENAKQQQDN--QFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSV--AVRNDDLYLTnig 143
Cdd:cd19973    28 LGIKLMTAAGKIDGDNatQVTAIENMIAAGAKGILITPSDTKAIVPAVKKARDAGVLVIALDTPTdpIDAADATFAT--- 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 sDFLHQGELAVEWLEDQTSDSEYVnILHLQGTYGATAQLMRTK--------AIEDAESTH--SNWKIV--AQLYGDftEA 211
Cdd:cd19973   105 -DNFKAGVLIGEWAKAALGAKDAK-IATLDLTPGHTVGVLRHQgflkgfgiDEKDPESNEdeDDSQVVgsADTNGD--QA 180
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1079631681 212 KGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGItygENGqVKIITFDATKTALQYCLDGKI 278
Cdd:cd19973   181 KGQTAMENLLQKDPDINLVYTINEPAAAGAYQALKAAGK---EKG-VLIVSVDGGCPGVKDVKDGII 243
PBP1_ABC_sugar_binding-like cd19965
monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; ...
76-286 1.09e-08

monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380620 [Multi-domain]  Cd Length: 272  Bit Score: 55.36  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  76 NAKQQQDNQFAAIRrfilEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRnDDLYLTNIGSDFLHQGE-LAV 154
Cdd:cd19965    41 DVAEQVSLLEAAIA----SGPDGIATTIVDPEAFDEVIKRALDAGIPVVAFNVDAPGG-ENARLAFVGQDLYPAGYvLGK 115
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 155 EWLEDQTSDSEYVNILHlqGTYGATAQLMRTKAIEDAEStHSNWKIVAQL--YGdFTEAKGYEVMTEYLKKNKDIDVLYS 232
Cdd:cd19965   116 RIAEKFKPGGGHVLLGI--STPGQSALEQRLDGIKQALK-EYGRGITYDVidTG-TDLAEALSRIEAYYTAHPDIKAIFA 191
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 233 ENDNMTFGAMRALDEAGItygeNGQVKIITFDATKTALQYCLDGKISLCVECNP 286
Cdd:cd19965   192 TGAFDTAGAGQAIKDLGL----KGKVLVGGFDLVPEVLQGIKAGYIDFTIDQQP 241
lacI PRK09526
lac repressor; Reviewed
194-266 1.70e-08

lac repressor; Reviewed


Pssm-ID: 181929 [Multi-domain]  Cd Length: 342  Bit Score: 55.00  E-value: 1.70e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1079631681 194 THSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGenGQVKIITFDAT 266
Cdd:PRK09526  208 TDYQLQPIAVREGDWSAMSGYQQTLQMLREGPVPSAILVANDQMALGVLRALHESGLRVP--GQISVIGYDDT 278
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
172-306 3.25e-08

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 54.11  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 172 LQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGIT 251
Cdd:PRK09701  162 IEGKAGNASGEARRNGATEAFKKASQIKLVASQPADWDRIKALDVATNVLQRNPNIKAIYCANDTMAMGVAQAVANAGKT 241
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1079631681 252 ygenGQVKIITFDATKTALQYCLDGKISLCVECNP-MHGPL-VEQLIKRYRSGETIP 306
Cdd:PRK09701  242 ----GKVLVVGTDGIPEARKMVEAGQMTATVAQNPaDIGATgLKLMVDAEKSGKVIP 294
PBP1_LuxPQ_Quorum_Sensing cd06303
periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi ...
79-249 6.09e-08

periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs; Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type 1 periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LuxPQ to control light production as well as its motility behavior.


Pssm-ID: 380526 [Multi-domain]  Cd Length: 320  Bit Score: 53.53  E-value: 6.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  79 QQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVII--IDRSVAVRNDDLYLTNIGSDFLHQGELAVEW 156
Cdd:cd06303    72 AEIRLQALQIREMLKSDPDYLIFTLDALRHRRFVEILLDSGKPKLILqnITTPLRDWDNHQPLLYVGFDHAEGSRMLAKH 151
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 157 LEDQTSDSEYVNILHlqGTYGATAQlMRTKAIEDAESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDN 236
Cdd:cd06303   152 FIKIFPEEGKYAILY--LTEGYVSD-QRGDTFIDEVARHSNLELVSAYYTDFDRESAREAARALLARHPDLDFIYACSTD 228
                         170
                  ....*....|...
gi 1079631681 237 MTFGAMRALDEAG 249
Cdd:cd06303   229 IALGAIDALQELG 241
PBP1_LacI-like cd06287
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
91-309 7.68e-08

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380510 [Multi-domain]  Cd Length: 268  Bit Score: 52.81  E-value: 7.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  91 FILEGVDL---IVIAPTIEegwDMILNEVQSAGIPVIIIDRSVAVRNDdlyltnigsdflhqgelaVEWLEDQTSDSEYV 167
Cdd:cd06287    50 SMLDALDVdgaIVVEPTVE---DPILARLRQRGVPVVSIGRAPGTDEP------------------VPYVDLQSAATARL 108
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 168 NILHLQGTyGA------TAQLMRTKAIEdAESTHSNW-------KIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSEN 234
Cdd:cd06287   109 LLEHLHGA-GArqvallTGSSRRNSSLE-SEAAYLRFaqeygttPVVYKVPESEGERAGYEAAAALLAAHPDIDAVCVPV 186
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 235 DNMTFGAMRALDEAGITYGEngQVKIIT-FDATK--------TALQYCLDGKISLCVEcnpmhgplveqLIKRYRSGETI 305
Cdd:cd06287   187 DAFAVGAMRAARDSGRSVPE--DLMVVTrYDGIRartadpplTAVDLHLDRVARTAID-----------LLFASLSGEER 253

                  ....
gi 1079631681 306 PKHV 309
Cdd:cd06287   254 SVEV 257
PBP1_methylthioribose_binding-like cd06305
similar to methylthioribose-binding protein of ABC-type transport systems that belong to a ...
69-317 1.07e-07

similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily; Proteins similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.


Pssm-ID: 380528 [Multi-domain]  Cd Length: 273  Bit Score: 52.30  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVI----APTIEEGWDMILNevqsAGIPVIIIDrsVAVRNDDLylTNIGS 144
Cdd:cd06305    29 GGTVIVFDANGDDARMADQIQQAITQKVDAIIIshgdADALDPKLKKALD----AGIPVVTFD--TDSQVPGV--NNITQ 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 DFLHQGELAVEWLEDQTSDSEyvNILHLQGTYGATAQlMRTKAIEDAESTHSNWKIVAQLYGDFTE---AKGYEVMTEYL 221
Cdd:cd06305   101 DDYALGTLSLGQLVKDLNGEG--NIAVFNVFGVPPLD-KRYDIYKAVLKANPGIKKIVAELGDVTPntaADAQTQVEALL 177
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 222 KKNKD--IDVLYSENDNMTFGAMRALDEAGITygengQVKIITFDATKTALQYCLD--GKISLCVECNP-MHGPLVEQLI 296
Cdd:cd06305   178 KKYPEggIDAIWAAWDEPAKGAVQALEEAGRT-----DIKVYGVDISNQDLELMADegSPWVATAAQDPaLIGTVAVRNV 252
                         250       260
                  ....*....|....*....|.
gi 1079631681 297 KRYRSGETIPKHVFIDEAAFT 317
Cdd:cd06305   253 ARKLAGEDLPDKYSLVPVLIT 273
PBP1_LsrB_Quorum_Sensing cd20003
ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic ...
82-292 1.12e-07

ligand-binding protein LsrB of ABC transporter periplasmic binding protein; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380658  Cd Length: 298  Bit Score: 52.28  E-value: 1.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  82 DNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTNIGSDFLhqGELAVEWLEDQT 161
Cdd:cd20003    43 SKQVEVINNFINQGYDVIAVSANDPDALAPALKKAMKKGIKVVTWDSDVNPDARDFFVNQATPEGI--GKTLVDMVAEQT 120
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 162 SDSEYVNILHlqGTYGATAQLMRTKAIEDA-ESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFG 240
Cdd:cd20003   121 GEKGKVAIVT--SSPTATNQNAWIKAMKAYiAEKYPDMKIVTTQYGQEDPAKSLQVAENILKAYPDLKAIIAPDSVALPG 198
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1079631681 241 AMRALDEAGITygenGQVKIITFDATKTALQYCLDGKISLCVECNPM-HGPLV 292
Cdd:cd20003   199 AAEAVEQLGRT----GKVAVTGLSTPNVMRPYVKDGTVKSVVLWDVVdLGYLA 247
PBP1_LsrB_Quorum_Sensing-like cd06302
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ...
66-276 2.71e-07

periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs; Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380525 [Multi-domain]  Cd Length: 296  Bit Score: 51.09  E-value: 2.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIEnAKQQQDN--QFAAIRRFILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTNIG 143
Cdd:cd06302    26 KELGVEVVYT-GPTQADAaqQVQIVENLIAQGVDAIAVSPNDADALAPVLKKAKDAGIKVITWDSDAPPSARDYFVNQAD 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 SDFLhqGELAVEWLEDQTSDSeyVNILHLQGTYGATAQLMRTKAIED-AESTHSNWKIVAQLYGDFTEAKGYEVMTEYLK 222
Cdd:cd06302   105 DEGL--GEALVDSLAKEIGGK--GKVAILSGSLTATNLNAWIKAMKEyLKSKYPDIELVDTYYTDDDQQKAYTQAQNLIQ 180
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 223 KNKDIDVLYSENDNMTFGAMRALDEAgityGENGQVKIITFDATKTALQYCLDG 276
Cdd:cd06302   181 AYPDLKGIIGVSTTAPPAAAQAVEEA----GKTGKVAVTGIGLPNTARPYLKDG 230
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
67-249 2.98e-07

Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356).


Pssm-ID: 395423 [Multi-domain]  Cd Length: 281  Bit Score: 50.97  E-value: 2.98e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIApTIEEGWDMILNEVQSAGIPVIIIDRsvaVRNDDLYLTNIGSDF 146
Cdd:pfam00532  29 DHGFDVFLLAVGDGEDTLTNAIDLLLASGADGIIIT-TPAPSGDDITAKAEGYGIPVIAADD---AFDNPDGVPCVMPDD 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 147 LHQGELAVEWLEDQTSDSEyvnILHLQGTYGATAQLMRTKAIEDAESTHS-NWKIVAQLYGDFTEAKGYEVMTEYLKKNK 225
Cdd:pfam00532 105 TQAGYESTQYLIAEGHKRP---IAVMAGPASALTARERVQGFMAALAAAGrEVKIYHVATGDNDIPDAALAANAMLVSHP 181
                         170       180
                  ....*....|....*....|....
gi 1079631681 226 DIDVLYSENDNMTFGAMRALDEAG 249
Cdd:pfam00532 182 TIDAIVAMNDEAAMGAVRALLKQG 205
PBP1_ABC_sugar_binding-like cd19966
monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; ...
66-280 3.93e-07

monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins; Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.


Pssm-ID: 380621 [Multi-domain]  Cd Length: 278  Bit Score: 50.79  E-value: 3.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIA-PTIEEGWDMILNEVQSAGIPVIIIDRSV-AVRNDDLYLTNIG 143
Cdd:cd19966    27 ADLGVDLDYVFSSWDPEKMVEQFKEAIAAKPDGIAIMgHPGDGAYTPLIEAAKKAGIIVTSFNTDLpKLEYGDCGLGYVG 106
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 SDFLHQG-ELAVEWLED---QTSDSEYVNILhlqgTYGATAQLMRTKAIEDA-ESTHSNWKIVAQLYGDFTEAKGYEVMT 218
Cdd:cd19966   107 ADLYAAGyTLAKELVKRgglKTGDRVFVPGL----LPGQPYRVLRTKGVIDAlKEAGIKVDYLEISLEPNKPAEGIPVMT 182
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079631681 219 EYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngqVKIITFDATKTALQYCLDGKISL 280
Cdd:cd19966   183 GYLAANPDVKAIVGDGGGLTANVAKYLKAAGKKPGE---IPVAGFDLSPATVQAIKSGYVNA 241
PBP1_CatR-like cd06296
ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in ...
67-269 3.01e-06

ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation; This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380519 [Multi-domain]  Cd Length: 270  Bit Score: 48.04  E-value: 3.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIE---NAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEgwdmiLNEVQSAGIPVIIIDrSVAVRNDDLylTNIG 143
Cdd:cd06296    27 AAGLDLVVTatrAGRAPVDDWVRRAVARGSAGVVLVTSDPTSRQ-----LRLLRSAGIPFVLID-PVGEPDPDL--PSVG 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 SDFLHQGELAVEWLedqtSDSEYVNILHLQGTYGATAQLMRT----KAIEDAESTHSNWKIvaqLYGDFTEAKGYEVMTE 219
Cdd:cd06296    99 ATNWAGGRLATEHL----LDLGHRRIAVITGPPRSVSGRARLagyrAALAEAGIAVDPDLV---REGDFTYEAGYRAARE 171
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1079631681 220 YLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTA 269
Cdd:cd06296   172 LLELPDPPTAVFAGNDEQALGVYRAARALGLRVPD--DLSVIGFDDTPPA 219
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
64-266 3.98e-06

Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold.


Pssm-ID: 380477 [Multi-domain]  Cd Length: 280  Bit Score: 47.65  E-value: 3.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  64 FTNDNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGwDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTNIG 143
Cdd:cd01391    27 TADKLGASVEIRDSCWHGSVALEQSIEFIRDNIAGVIGPGSSSVA-IVIQNLAQLFDIPQLALDATSQDLSDKTLYKYFL 105
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 144 S---DFLHQGELAVEWLEDQTSdsEYVNILHlqGTYGATAQLMRTKAIEDAesTHSNWKIVAQLYGD-FTEAKGYEVMTE 219
Cdd:cd01391   106 SvvfSDTLGARLGLDIVKRKNW--TYVAAIH--GEGLNSGELRMAGFKELA--KQEGICIVASDKADwNAGEKGFDRALR 179
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1079631681 220 YLKKNKDIDVLYSENDNMTFGAMRALDEAGItygeNGQVKIITFDAT 266
Cdd:cd01391   180 KLREGLKARVIVCANDMTARGVLSAMRRLGL----VGDVSVIGSDGW 222
PBP1_sucrose_transcription_regulator cd06288
ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members ...
67-264 5.61e-06

ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380511 [Multi-domain]  Cd Length: 268  Bit Score: 47.16  E-value: 5.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEEgwdmILNEVQSAGIPVIIIDrsvAVRNDDLYLTNIGSD 145
Cdd:cd06288    28 EHGYLLLLANTGGDPELEAEAIRELLSRRVDgIIYASMHHRE----VTLPPELTDIPLVLLN---CFDDDPSLPSVVPDD 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 146 FlHQGELAVEWLEDQTsdseYVNILHLQGTYGATAQLMRTKAIEDAESTH-----SNWkivaQLYGDFTEAKGYEVMTEY 220
Cdd:cd06288   101 E-QGGYLATRHLIEAG----HRRIAFIGGPEDSLATRLRLAGYRAALAEAgipydPSL----VVHGDWGRESGYEAAKRL 171
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1079631681 221 LKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06288   172 LSAPDRPTAIFCGNDRMAMGVYQAAAELGLRVPE--DLSVVGFD 213
PBP1_AglR-like cd20010
Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and ...
59-273 6.63e-06

Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins; Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380665 [Multi-domain]  Cd Length: 269  Bit Score: 46.78  E-value: 6.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  59 SMSQTFtNDNGYELIIENAKQQQDnQFAAIRRFILEG-VD-LIVIAPTIEegwDMILNEVQSAGIPVIIIDRSVavRND- 135
Cdd:cd20010    24 GLSEAL-AERGLDLLLAPAPSGED-ELATYRRLVERGrVDgFILARTRVN---DPRIAYLLERGIPFVVHGRSE--SGAp 96
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 136 ----DLyltnigsDFLHQGELAVEWLEDQTSDseyvNILHLQGTYGATAQLMRTKAIEDAESTH-----SNWkivaQLYG 206
Cdd:cd20010    97 yawvDI-------DNEGAFRRATRRLLALGHR----RIALLNGPEELNFAHQRRDGYRAALAEAglpvdPAL----VREG 161
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1079631681 207 DFTEAKGYEVMTEYLKKNKDID-VLYSeNDNMTFGAMRALDEAGITYGENgqVKIITFDATKTALQYC 273
Cdd:cd20010   162 PLTEEGGYQAARRLLALPPPPTaIVCG-SDLLALGAYRALREAGLSPGKD--VSVIGHDDLLPALEYF 226
PBP1_AglR_RafR-like cd06292
Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that ...
206-269 4.17e-05

Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the repressors specific raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins highly similar to DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR). Members of this group belong to the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380515 [Multi-domain]  Cd Length: 273  Bit Score: 44.57  E-value: 4.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1079631681 206 GDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGenGQVKIITFDATKTA 269
Cdd:cd06292   161 GENTEEGGYAAAARLLDLGPPPTAIVCVSDLLALGAMRAARERGLRVG--RDVSVVGFDDSPLA 222
PBP1_LacI-like cd06284
ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus ...
68-273 5.77e-05

ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria; This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.


Pssm-ID: 380507 [Multi-domain]  Cd Length: 267  Bit Score: 44.07  E-value: 5.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELIIENAKQQQDNQFAAIRRFILEGVD-LIVIAPTIEEGWDMILNE----VQ------SAGIPVIIIDRSVAVRNDD 136
Cdd:cd06284    28 AGYDVLLGDTDSDPEREDDLLDMLRSRRVDgVILLSGRLDAELLSELSKrypiVQcceyipDSGVPSVSIDNEAAAYDAT 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 137 LYLTNIGsdflHQgelavewledqtsdseyvNILHLQG--TYGATAQLMR--TKAIEDAES-THSNWKIVaqlyGDFTEA 211
Cdd:cd06284   108 EYLISLG----HR------------------RIAHINGplDNVYARERLEgyRRALAEAGLpVDEDLIIE----GDFSFE 161
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1079631681 212 KGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTAlQYC 273
Cdd:cd06284   162 AGYAAARALLALPERPTAIFCASDELAIGAIKALRRAGLRVPE--DVSVIGFDDIEFA-EMF 220
PRK10703 PRK10703
HTH-type transcriptional repressor PurR;
69-269 2.26e-04

HTH-type transcriptional repressor PurR;


Pssm-ID: 236739 [Multi-domain]  Cd Length: 341  Bit Score: 42.40  E-value: 2.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVD--LIVIAPTIEEGWDMiLNEVQSagIPVIIIDRSVAvRND--DLYLTNIgs 144
Cdd:PRK10703   89 GYTLILCNAWNNLEKQRAYLSMLAQKRVDglLVMCSEYPEPLLAM-LEEYRH--IPMVVMDWGEA-KADftDAIIDNA-- 162
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 145 dfLHQGELAVEWLEDQTSDSEYVNILHLQGTYGATAQLMRTKAIEDAEST-HSNWkIVAqlyGDFTEAKGYEVMTEYLKK 223
Cdd:PRK10703  163 --FEGGYLAGRYLIERGHRDIGVIPGPLERNTGAGRLAGFMKAMEEANIKvPEEW-IVQ---GDFEPESGYEAMQQILSQ 236
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1079631681 224 NKDIDVLYSENDNMTFGAMRALDEAGITYGENgqVKIITFDATKTA 269
Cdd:PRK10703  237 KHRPTAVFCGGDIMAMGAICAADEMGLRVPQD--ISVIGYDNVRNA 280
PBP1_ABC_rhamnose cd20000
rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding ...
92-260 3.35e-04

rhamnose ABC transporter substrate-binding protein; Rhamnose ABC transporter substrate-binding protein similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling.


Pssm-ID: 380655  Cd Length: 298  Bit Score: 41.86  E-value: 3.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  92 ILEGVDLIVIAPTIEEGWDMILNEVQSAGIPVIIIDRSVAVRNDDLYLTNIGSDFLhqGELAVEWLEDQTSDSEYVNILh 171
Cdd:cd20000    53 IQQGVDAIAISANDPDALAPALKKARAAGIKVVTFDSDVAPEARDLFVNQADADGI--GRAQVDMMAELIGGEGEFAIL- 129
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 172 lQGTYGATAQLMRTKAIED--AESTHSNWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENdnmTFG---AMRALD 246
Cdd:cd20000   130 -SATPTATNQNAWIDAMKKelASPEYAGMKLVKVAYGDDDAQKSYQEAEALLQAYPDLKGIIAPT---TVGiaaAARALE 205
                         170
                  ....*....|....
gi 1079631681 247 EAGITygenGQVKI 260
Cdd:cd20000   206 DSGLK----GKVKV 215
PBP1_AraR cd01541
ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a ...
67-264 4.10e-04

ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380483 [Multi-domain]  Cd Length: 274  Bit Score: 41.39  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  67 DNGYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPT------IEEGwdmILNEVQSAGIPVIIIDRS------VAVRN 134
Cdd:cd01541    27 ENGYSLLLALTNNDVEKEREILESLLDQNVDGLIIEPTksalpnPNLD---LYEELQKKGIPVVFINSYypeldaPSVSL 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 135 DDLYLtnigsdflhqGELAVEWLEDQ---------TSDseyvnilHLQGtygataqLMRTKAIEDAESTHS----NWKIV 201
Cdd:cd01541   104 DDEKG----------GYLATKHLIDLghrriagifKSD-------DLQG-------VERYQGFIKALREAGlpidDDRIL 159
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 202 AQLYGDFTEAKGYEVMTEYLKKNKDID--VLYseNDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd01541   160 WYSTEDLEDRFFAEELREFLRRLSRCTaiVCY--NDEIALRLIQALREAGLRVPE--DLSVVGFD 220
PRK11303 PRK11303
catabolite repressor/activator;
69-224 5.65e-04

catabolite repressor/activator;


Pssm-ID: 236897 [Multi-domain]  Cd Length: 328  Bit Score: 41.02  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  69 GYELIIENAKQQQDNQFAAIRRFILEGVDLIVIAPTIEEGWDMILNeVQSAGIPVIIIDRSVavrNDDLYLTNIGSDFLH 148
Cdd:PRK11303   91 GYQLLIACSDDQPDNEMRCAEHLLQRQVDALIVSTSLPPEHPFYQR-LQNDGLPIIALDRAL---DREHFTSVVSDDQDD 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 149 QGELAVEWLEDQtsdseYVNILHLqgtyGATAQL----MRTKAIEDAESTHSNwkIVAQLYGD-FTEAKGYEVMTEYLKK 223
Cdd:PRK11303  167 AEMLAESLLKFP-----AESILLL----GALPELsvsfEREQGFRQALKDDPR--EVHYLYANsFEREAGAQLFEKWLET 235

                  .
gi 1079631681 224 N 224
Cdd:PRK11303  236 H 236
PBP1_SalR cd01545
ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of ...
66-250 7.82e-04

ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators; Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380487 [Multi-domain]  Cd Length: 270  Bit Score: 40.62  E-value: 7.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  66 NDNGYELIIENAKQQQDNQFAAIRRFILE-GVD-LIVIAPTIEEGWdmILNEVQSAGIPVIII------DRSVAVRNDDL 137
Cdd:cd01545    26 REAGYHLVVEPCDSDDEDLADRLRRFLSRsRPDgVILTPPLSDDPA--LLDALDELGIPYVRIapgtddDRSPSVRIDDR 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 138 yltnigsdflHQGELAVEWLEDQ--TSdseyvnILHLQG--TYGATAQ-------LMRTKAIEDAESthsnwkIVAQlyG 206
Cdd:cd01545   104 ----------AAAREMTRHLIALghRR------IGFIAGppDHGASAErlegfrdALAEAGLPLDPD------LVVQ--G 159
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1079631681 207 DFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGI 250
Cdd:cd01545   160 DFTFESGLEAAEALLDLPDRPTAIFASNDEMAAGVLAAAHRLGL 203
PBP1_LacI-like cd06277
ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of ...
68-264 8.77e-04

ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors; This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380500 [Multi-domain]  Cd Length: 275  Bit Score: 40.30  E-value: 8.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  68 NGYELII----------ENAKQQQDNQFAAIrrfILEGVDLiviapTIEEgwdmiLNEVQSAGIPVIIIDRSVAVRNDDL 137
Cdd:cd06277    35 YGYNLLIssvdigddfdEILKELTDDQSSGI---ILLGTEL-----EEKQ-----IKLFQDVSIPVVVVDNYFEDLNFDC 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 138 YLT-NIGSDFLhqgelAVEWLEDQTsdseYVNILHLQGTYGATAQLMRTKAIEDAESTHSNWKIVAQLYG---DFTEAkg 213
Cdd:cd06277   102 VVIdNEDGAYE-----AVKYLVELG----HTRIGYLASSYRIKNFEERRRGFRKAMRELGLSEDPEPEFVvsvGPEGA-- 170
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1079631681 214 YEVMTEYL-KKNKDIDVLYSENDNMTFGAMRALDEAGITYgeNGQVKIITFD 264
Cdd:cd06277   171 YKDMKALLdTGPKLPTAFFAENDIIALGCIKALQEAGIRV--PEDVSVIGFD 220
PBP1_RegR_EndR_KdgR-like cd06283
ligand-binding domain of DNA transcription repressor RegR and other putative regulators such ...
58-264 1.34e-03

ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR; Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.


Pssm-ID: 380506 [Multi-domain]  Cd Length: 266  Bit Score: 39.84  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681  58 KSMSQTFtNDNGYELII----ENAKQQQDNqfaaIRRFILEGVDLIVIAPTIEEGWDMIlnEVQSAGIPVIIIDRSVavr 133
Cdd:cd06283    19 KGIEDVC-REAGYQLLIcnsnNDPEKERDY----IESLLSQRVDGLILQPTGNNNDAYL--ELAQKGLPVVLVDRQI--- 88
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 134 nDDLYLTNIGSDflhqGELAVEWLEDQTSDSEYVNILHLQGTYGA-TAQLMRTKAIEDAESTHSNWK---IVAQLYGDFT 209
Cdd:cd06283    89 -EPLNWDTVVTD----NYDATYEATEHLKEQGYERIVFVTEPIKGiSTRRERLQGFLDALARYNIEGdvyVIEIEDTEDL 163
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 210 EAKGYEVMTEYLKKNKdidVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06283   164 QQALAAFLSQHDGGKT---AIFAANGVVLLRVLRALKALGIRIPD--DVGLCGFD 213
PRK10339 PRK10339
DNA-binding transcriptional repressor EbgR; Provisional
206-311 1.88e-03

DNA-binding transcriptional repressor EbgR; Provisional


Pssm-ID: 182389 [Multi-domain]  Cd Length: 327  Bit Score: 39.74  E-value: 1.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 206 GDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFDATKTAlQYCLDGKISLCVECN 285
Cdd:PRK10339  214 GGFSSSSGYELAKQMLAREDYPKALFVASDSIAIGVLRAIHERGLNIPQ--DISLISVNDIPTA-RFTFPPLSTVRIHSE 290
                          90       100
                  ....*....|....*....|....*.
gi 1079631681 286 PMHGPLVEQLIKRYRSGETIPKHVFI 311
Cdd:PRK10339  291 MMGSQGVNLLYEKARDGRALPLLVFV 316
PBP1_CcpB-like cd06286
ligand-binding domain of a novel transcription factor implicated in catabolite repression in ...
114-264 1.95e-03

ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species; This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. Catabolite control protein B (CcpB) is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree.


Pssm-ID: 380509 [Multi-domain]  Cd Length: 262  Bit Score: 39.07  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1079631681 114 NEVQSAGIPVIIIDRsvavrnddlyltnigsdflHQG-ELAVEWLEDQtsdsEYVNILHLQG--TYGATAQLMRTKAIED 190
Cdd:cd06286    84 EETDSPDIPSVYIDR-------------------YEAyLEALEYLKEK----GHRKIGYCLGrpESSSASTQARLKAYQD 140
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1079631681 191 AESTHS-NWKIVAQLYGDFTEAKGYEVMTEYLKKNKDIDVLYSENDNMTFGAMRALDEAGITYGEngQVKIITFD 264
Cdd:cd06286   141 VLGEHGlSLREEWIFTNCHTIEDGYKLAKKLLALKERPDAIFTNSDEVAAGIIAEAQKNGIRVPE--DLAVIGFD 213
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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