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Conserved domains on  [gi|309274435|gb|ADO63849|]
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AraF [Cloning vector pKaKa2]

Protein Classification

arabinose ABC transporter substrate-binding protein( domain architecture ID 10107481)

arabinose ABC transporter substrate-binding protein serves as the initial receptor in the high-affinity L-arabinose membrane transport system

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 41-335 1.29e-134

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: 384.72  E-value: 1.29e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKFVTVDDQLVDSSGKPLanVPHLGMSATKIGNQVGQAIADEMKKRGW-KPEEVGALRVTNYELPTAKLRTDGATQALLA 198
Cdd:cd01540   81 IPVIAVDDQLVDADPMKI--VPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 SGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKKWVIFALNEETVLGAVRATEQLHIPAADVIGVGInGAGEAFAEF 278
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGI-GGYLAADEE 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 309274435 279 QKKEPTGFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPPADTQTSGKLMTRENWQAVR 335
Cdd:cd01540  238 FKKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAETLTDGVIVTRDNYKEVM 294
 
Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 41-335 1.29e-134

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: 384.72  E-value: 1.29e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKFVTVDDQLVDSSGKPLanVPHLGMSATKIGNQVGQAIADEMKKRGW-KPEEVGALRVTNYELPTAKLRTDGATQALLA 198
Cdd:cd01540   81 IPVIAVDDQLVDADPMKI--VPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 SGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKKWVIFALNEETVLGAVRATEQLHIPAADVIGVGInGAGEAFAEF 278
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGI-GGYLAADEE 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 309274435 279 QKKEPTGFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPPADTQTSGKLMTRENWQAVR 335
Cdd:cd01540  238 FKKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAETLTDGVIVTRDNYKEVM 294
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
 40-329 8.84e-36

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: 131.09  E-value: 8.84e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435   40 LKIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTPDGEKVLA-AIDNLGSQGAQGFVICAPDVRlGPAIAARAKRY 118
Cdd:pfam00532   2 LKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLTnAIDLLLASGADGIIITTPAPS-GDDITAKAEGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  119 DMKFVTVDDQLVDSSGkplanVPHLGMSATKIGNQVGQAIADEMKKRG--WKPEEVGALrvtnyelpTAKLRTDGATQAL 196
Cdd:pfam00532  81 GIPVIAADDAFDNPDG-----VPCVMPDDTQAGYESTQYLIAEGHKRPiaVMAGPASAL--------TARERVQGFMAAL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  197 LASGFKKEnIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATE-QLHIPAADVIGVGINGAgEAF 275
Cdd:pfam00532 148 AAAGREVK-IYHVATGDNDIPDAALAANAMLVSHPTID--AIVAMNDEAAMGAVRALLkQGRVKIPDIVGIGINSV-VGF 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435  276 AEFQKKEPTGFFGT-IAVSSTNH---GKQSAQNLVDWIRSGKAPPADTQTSGKLMTRE 329
Cdd:pfam00532 224 DGLSKAQDTGLYLSpLTVIQLPRqllGIKASDMVYQWIPKFREHPRVLLIPRDFFKET 281
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 16-330 1.35e-34

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: 128.50  E-value: 1.35e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  16 LRAAFAALVIAPLAMPAATRADTPLKIGFLVKMPEQAWFINEQKAATALGQKEGFSV-VNIGTPDGEKVLAAIDNLGSQG 94
Cdd:COG1879   10 LALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELiVVDAEGDAAKQISQIEDLIAQG 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  95 AQGFVICAPDVRLGPAIAARAKRYDMKFVTVDDQLVDSsgkplANVPHLGMSATKIGNQVGQAIADEMKKRGwkpeEVGA 174
Cdd:COG1879   90 VDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDVDGS-----DRVAYVGSDNYAAGRLAAEYLAKALGGKG----KVAI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 175 LRVTNyELPTAKLRTDGATQALlaSGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATE 254
Cdd:COG1879  161 LTGSP-GAPAANERTDGFKEAL--KEYPGIKVVAEQYADWDREKALEVMEDLLQAHPDID--GIFAANDGMALGAAQALK 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 309274435 255 QLHIpAADVIGVGINGAGEAFAEFQKKEptgFFGTIAVSSTNHGKQSAQNLVDWIRsGKAPPADTQTSGKLMTREN 330
Cdd:COG1879  236 AAGR-KGDVKVVGFDGSPEALQAIKDGT---IDATVAQDPYLQGYLAVDAALKLLK-GKEVPKEILTPPVLVTKEN 306
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
66-318 7.95e-05

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 43.71  E-value: 7.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  66 QKEGFSVVNIGTP---DGEKVLAAIDNLGSQGAQGFVIcAP--DVRLGPAIAaRAKRYDMKFVTVDDQL-VDSSGKPLAN 139
Cdd:PRK09701  51 KTLGVSVDIFASPsegDFQSQLQLFEDLSNKNYKGIAF-APlsSVNLVMPVA-RAWKKGIYLVNLDEKIdMDNLKKAGGN 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 140 VphLGMSAT---KIGNQVGQAIADEMKKRGwkpeevGALRVTNYELPTA--KLRTDGATQALLASGFKKenIFDAPQKTT 214
Cdd:PRK09701 129 V--EAFVTTdnvAVGAKGASFIIDKLGAEG------GEVAIIEGKAGNAsgEARRNGATEAFKKASQIK--LVASQPADW 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 215 DDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHiPAADVIGVGINGAGEAFAEFQKKEPTGffgTIAVSS 294
Cdd:PRK09701 199 DRIKALDVATNVLQRNPNIK--AIYCANDTMAMGVAQAVANAG-KTGKVLVVGTDGIPEARKMVEAGQMTA---TVAQNP 272

                        250       260
                 ....*....|....*....|....
gi 309274435 295 TNHGKQSAQNLVDWIRSGKAPPAD 318
Cdd:PRK09701 273 ADIGATGLKLMVDAEKSGKVIPLD 296
 
Name Accession Description Interval E-value
PBP1_arabinose_binding cd01540
periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose ...
 41-335 1.29e-134

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: 384.72  E-value: 1.29e-134
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd01540    1 KIGFIVKQPDQPWFQDEWKGAKKAAKELGFEVIKIDAKmDGEKVLSAIDNLIAQGAQGIVICTPDQKLGPAIAAKAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKFVTVDDQLVDSSGKPLanVPHLGMSATKIGNQVGQAIADEMKKRGW-KPEEVGALRVTNYELPTAKLRTDGATQALLA 198
Cdd:cd01540   81 IPVIAVDDQLVDADPMKI--VPFVGIDAYKIGEAVGEWLAKEMKKRGWdDVKEVGVLAITMDTLSVCVDRTDGAKDALKA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 SGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKKWVIFALNEETVLGAVRATEQLHIPAADVIGVGInGAGEAFAEF 278
Cdd:cd01540  159 AGFPEDQIFQAPYKGTDTEGAFNAANAVITAHPEVKHWLVVGCNDEGVLGAVRALEQAGFDAEDIIGVGI-GGYLAADEE 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 309274435 279 QKKEPTGFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPPADTQTSGKLMTRENWQAVR 335
Cdd:cd01540  238 FKKQPTGFKASLYISPDKHGYIAAEELYNWITDGKPPPAETLTDGVIVTRDNYKEVM 294
Peripla_BP_1 pfam00532
Periplasmic binding proteins and sugar binding domain of LacI family; This family includes the ...
 40-329 8.84e-36

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: 131.09  E-value: 8.84e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435   40 LKIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTPDGEKVLA-AIDNLGSQGAQGFVICAPDVRlGPAIAARAKRY 118
Cdd:pfam00532   2 LKLGALVPQLDEPFFQDLVKGITKAAKDHGFDVFLLAVGDGEDTLTnAIDLLLASGADGIIITTPAPS-GDDITAKAEGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  119 DMKFVTVDDQLVDSSGkplanVPHLGMSATKIGNQVGQAIADEMKKRG--WKPEEVGALrvtnyelpTAKLRTDGATQAL 196
Cdd:pfam00532  81 GIPVIAADDAFDNPDG-----VPCVMPDDTQAGYESTQYLIAEGHKRPiaVMAGPASAL--------TARERVQGFMAAL 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  197 LASGFKKEnIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATE-QLHIPAADVIGVGINGAgEAF 275
Cdd:pfam00532 148 AAAGREVK-IYHVATGDNDIPDAALAANAMLVSHPTID--AIVAMNDEAAMGAVRALLkQGRVKIPDIVGIGINSV-VGF 223

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435  276 AEFQKKEPTGFFGT-IAVSSTNH---GKQSAQNLVDWIRSGKAPPADTQTSGKLMTRE 329
Cdd:pfam00532 224 DGLSKAQDTGLYLSpLTVIQLPRqllGIKASDMVYQWIPKFREHPRVLLIPRDFFKET 281
RbsB COG1879
ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH ...
 16-330 1.35e-34

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: 128.50  E-value: 1.35e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  16 LRAAFAALVIAPLAMPAATRADTPLKIGFLVKMPEQAWFINEQKAATALGQKEGFSV-VNIGTPDGEKVLAAIDNLGSQG 94
Cdd:COG1879   10 LALALALAACGSAAAEAAAAAAKGKTIGFVVKTLGNPFFVAVRKGAEAAAKELGVELiVVDAEGDAAKQISQIEDLIAQG 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  95 AQGFVICAPDVRLGPAIAARAKRYDMKFVTVDDQLVDSsgkplANVPHLGMSATKIGNQVGQAIADEMKKRGwkpeEVGA 174
Cdd:COG1879   90 VDAIIVSPVDPDALAPALKKAKAAGIPVVTVDSDVDGS-----DRVAYVGSDNYAAGRLAAEYLAKALGGKG----KVAI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 175 LRVTNyELPTAKLRTDGATQALlaSGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATE 254
Cdd:COG1879  161 LTGSP-GAPAANERTDGFKEAL--KEYPGIKVVAEQYADWDREKALEVMEDLLQAHPDID--GIFAANDGMALGAAQALK 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 309274435 255 QLHIpAADVIGVGINGAGEAFAEFQKKEptgFFGTIAVSSTNHGKQSAQNLVDWIRsGKAPPADTQTSGKLMTREN 330
Cdd:COG1879  236 AAGR-KGDVKVVGFDGSPEALQAIKDGT---IDATVAQDPYLQGYLAVDAALKLLK-GKEVPKEILTPPVLVTKEN 306
PBP1_ABC_sugar_binding-like cd01536
periplasmic sugar-binding domain of active transport systems that are members of the type 1 ...
 41-316 7.75e-24

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: 98.41  E-value: 7.75e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd01536    1 KIGVVVKDLTNPFWVAVKKGAEAAAKELGVELVVLDAQgDVAKQISQIEDLIAQGVDAIIIAPVDSEALVPAVKKANAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKFVTVDDQlVDSSGKPLANVphlGMSATKIGNQVGQAIADEMKKRGwkpeEVGALRVTNYElPTAKLRTDGATQAlLAS 199
Cdd:cd01536   81 IPVVAVDTD-IDGGGDVVAFV---GTDNYEAGKLAGEYLAEALGGKG----KVAILEGPPGS-STAIDRTKGFKEA-LKK 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 200 GFKKENIFDAPQKtTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHIpAADVIGVGINGAGEAFAEFQ 279
Cdd:cd01536  151 YPDIEIVAEQPAN-WDRAKALTVTENLLQANPDID--AVFAANDDMALGAAEALKAAGR-TGDIKIVGVDGTPEALKAIK 226

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 309274435 280 KKEptgFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPP 316
Cdd:cd01536  227 DGE---LDATVAQDPYLQGYLAVEAAVKLLNGEKVPK 260
PBP1_ABC_D-talitol-like cd06318
periplasmic D-talitol-binding protein of an ABC transport system and similar proteins; ...
 41-330 1.68e-11

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: 63.97  E-value: 1.68e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNI-GTPDGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd06318    1 KIGFSQRTLASPYYAALVAAAKAEAKKLGVELVVTdAQNDLTKQISDVEDLITRGVDVLILNPVDPEGLTPAVKAAKAAG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKFVTVDDQLvDSSGKPLANVphlGMSATKIGNQVGQAIADEMKKRGWKPEEVGAlrvtNYELPTAKLRTDG-----ATQ 194
Cdd:cd06318   81 IPVITVDSAL-DPSANVATQV---GRDNKQNGVLVGKEAAKALGGDPGKIIELSG----DKGNEVSRDRRDGflagvNEY 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 195 ALLASGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHIpAADVIGVGINGAGEA 274
Cdd:cd06318  153 QLRKYGKSNIKVVAQPYGNWIRSGAVAAMEDLLQAHPDIN--VVYAENDDMALGAMKALKAAGM-LDKVKVAGADGQKEA 229

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 309274435 275 faeFQKKEPTGFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPPADTQTSGKLMTREN 330
Cdd:cd06318  230 ---LKLIKDGKYVATGLNDPDLLGKTAVDTAAKVVKGEESFPEFTYTPTALITKDN 282
PBP1_ABC_sugar_binding-like cd06319
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 41-274 2.40e-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: 380542 [Multi-domain]  Cd Length: 278  Bit Score: 60.45  E-value: 2.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTPDGEKVLAA-IDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd06319    1 KIGYSVYDLDNPFWQIMERGVQAAAEELGYEFVTYDQKNSANEQVTnANDLIAQGVDGIIISPTNSSAAPTVLDLANEAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 120 MKfVTVDDqLVDSSGKPLANVphlgMSATKIGN-QVGQAIADEMKKRGWKPEEVGALRVTnyelPTAK---LRTDGATQA 195
Cdd:cd06319   81 IP-VVIAD-IGTGGGDYVSYI----ISDNYDGGyQAGEYLAEALKENGWGGGSVGIIAIP----QSRVngqARTAGFEDA 150

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 309274435 196 LLASGFKKENIFDAPQKTTDDegGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHIpAADVIGVGINGAGEA 274
Cdd:cd06319  151 LEEAGVEEVALRQTPNSTVEE--TYSAAQDLLAANPDIK--GIFAQNDQMAQGALQAIEEAGR-TGDILVVGFDGDPEA 224
Peripla_BP_4 pfam13407
Periplasmic binding protein domain; This domain is found in a variety of bacterial periplasmic ...
 42-307 2.19e-09

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: 57.32  E-value: 2.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435   42 IGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIG--TPDGEKVLAAIDNLGSQGAQGFVICAPDV-RLGPAIaARAKRY 118
Cdd:pfam13407   1 IGVVPKSTGNPFFQAAEEGAEEAAKELGGEVIVVGpaEADAAEQVAQIEDAIAQGVDAIIVAPVDPtALAPVL-KKAKDA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  119 DMKFVTVDDQLVDSSGkplanVPHLGMSATKIGNQVGQAIADEMKKRGwkpeEVGALRVtNYELPTAKLRTDGATQAlLA 198
Cdd:pfam13407  80 GIPVVTFDSDAPSSPR-----LAYVGFDNEAAGEAAGELLAEALGGKG----KVAILSG-SPGDPNANERIDGFKKV-LK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  199 SGFKKENIFDAPQKTTDD-EGGFSAAAPVLARHPNVKKwVIFALNEETVLGAVRATEQLHIpaADVIGVGINGAGEAFAE 277
Cdd:pfam13407 149 EKYPGIKVVAEVEGTNWDpEKAQQQMEALLTAYPNPLD-GIISPNDGMAGGAAQALEAAGL--AGKVVVTGFDATPEALE 225

                         250       260       270
                  ....*....|....*....|....*....|
gi 309274435  278 FQKKEptGFFGTIAVSSTNHGKQSAQNLVD 307
Cdd:pfam13407 226 AIKDG--TIDATVLQDPYGQGYAAVELAAA 253
PBP1_ABC_sugar_binding-like cd19970
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 41-252 7.89e-09

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: 55.72  E-value: 7.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAA-TALGQKEGFSVVNIGTP---DGEKVLAAIDNLGSQGAQGFVICAPD-VRLGPAIAaRA 115
Cdd:cd19970    1 KVALVMKSLANEFFIEMEKGArKHAKEANGYELLVKGIKqetDIEQQIAIVENLIAQKVDAIVIAPADsKALVPVLK-KA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 116 KRYDMKFVTVDDQL-VDSSGKPLANVPHLGMSATKIGNQVGQAIADEMKKrgwkPEEVGALR----VTNyelptAKLRTD 190
Cdd:cd19970   80 VDAGIAVINIDNRLdADALKEGGINVPFVGPDNRQGAYLAGDYLAKKLGK----GGKVAIIEgipgADN-----AQQRKA 150

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 309274435 191 GATQALLASGFKkenIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRA 252
Cdd:cd19970  151 GFLKAFEEAGMK---IVASQSANWEIDEANTVAANLLTAHPDIR--GILCANDNMALGAIKA 207
Periplasmic_Binding_Protein_type1 cd01391
Type 1 periplasmic binding fold superfamily; Type 1 periplasmic binding fold superfamily. This ...
 50-274 7.91e-09

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: 55.74  E-value: 7.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  50 EQAWfINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVICAP-DVRLgpAIAARAKRYDMKFVTVDD 127
Cdd:cd01391   14 EQFG-IQRVEAIFHTADKLGASVEIRDSCwHGSVALEQSIEFIRDNIAGVIGPGSsSVAI--VIQNLAQLFDIPQLALDA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 128 QLVDSSGKPLANVPhlgMSATKIGNQVGQAIADEMKKRGWkpEEVGAlrVTNYELPTAKLRTDGATQALLASGFKKenIF 207
Cdd:cd01391   91 TSQDLSDKTLYKYF---LSVVFSDTLGARLGLDIVKRKNW--TYVAA--IHGEGLNSGELRMAGFKELAKQEGICI--VA 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 309274435 208 DAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHIpAADVIGVGINGAGEA 274
Cdd:cd01391  162 SDKADWNAGEKGFDRALRKLREGLKAR--VIVCANDMTARGVLSAMRRLGL-VGDVSVIGSDGWADR 225
PBP1_ABC_sugar_binding-like cd06322
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 59-316 9.75e-09

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: 55.36  E-value: 9.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  59 KAATALGQKegfSVVNIGTPDGEKVLAAIDNLGSQGAQGFVICAPDVR-LGPAIAArAKRYDMKFVTVDDQLvdSSGKPl 137
Cdd:cd06322   23 KEAAELGVK---VVVADANGDLAKQLSQIEDFIQQGVDAIILAPVDSGgIVPAIEA-ANEAGIPVFTVDVKA--DGAKV- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 138 anVPHLGMSATKIGNQVGQAIADEMKKRGWKpeevgALRVTNYELPTAKLRTDGATQALlaSGFKKENIFDAPQKTTDDE 217
Cdd:cd06322   96 --VTHVGTDNYAGGKLAGEYALKALLGGGGK-----IAIIDYPEVESVVLRVNGFKEAI--KKYPNIEIVAEQPGDGRRE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 218 GGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHiPAADVIGVGINGAGEAFAEFQKKEPtgFFGTIAVSSTNH 297
Cdd:cd06322  167 EALAATEDMLQANPDLD--GIFAIGDPAALGALTAIESAG-KEDKIKVIGFDGNPEAIKAIAKGGK--IKADIAQQPDKI 241

                        250
                 ....*....|....*....
gi 309274435 298 GKQSAQNLVDWIRSGKAPP 316
Cdd:cd06322  242 GQETVEAIVKYLAGETVEK 260
PBP1_allose_binding cd06320
periplasmic allose-binding domain of bacterial transport systems that function as a primary ...
 41-330 1.82e-08

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: 54.96  E-value: 1.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP---DGEKVLAAIDNLGSQGAQGFVIcAP--DVRLGPAIAaRA 115
Cdd:cd06320    1 KIGVVLKTLSNPFWVAMKDGIEAEAKKLGVKVDVQAAPsetDTQGQLNLLETMLNKGYDAILV-SPisDTNLIPPIE-KA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 116 KRYDMKFVTVDDQL-VDSSGKPLANV-PHLGMSATKIGNQVGQAIADEMKKRGwkpeEVGALR--VTNYelpTAKLRTDG 191
Cdd:cd06320   79 NKKGIPVINLDDAVdADALKKAGGKVtSFIGTDNVAAGALAAEYIAEKLPGGG----KVAIIEglPGNA---AAEARTKG 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 192 ATqallaSGFKKENIFDAPQKTT---DDEGGFSAAAPVLARHPNVKKwvIFALNEETVLGAVRAteqlhIPAAD----VI 264
Cdd:cd06320  152 FK-----ETFKKAPGLKLVASQPadwDRTKALDAATAILQAHPDLKG--IYAANDTMALGAVEA-----VKAAGktgkVL 219

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 309274435 265 GVGINGAGEAFAEFQKKEPTgffGTIAVSSTNHGKQSAQNLVdWIRSGKAPPADTQTSGKLMTREN 330
Cdd:cd06320  220 VVGTDGIPEAKKSIKAGELT---ATVAQYPYLEGAMAVEAAL-RLLQGQKVPAVVATPQALITKDN 281
PBP1_ABC_IbpA-like cd19968
periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins; The ...
 41-315 4.48e-08

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: 53.54  E-value: 4.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNI-GTPDGEKVLAAIDNLGSQGAQGFVICAPDVR-LGPAIAARAKRy 118
Cdd:cd19968    1 KIGFSFPNLSFPFFVYMHEQAVDEAAKLGVKLVVLdAQNSSSKQASDLENAIAQGVDGIIVSPIDVKaLVPAIEAAIKA- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 119 DMKFVTVDDQlVDSSgkplANVPHLGMSATKIGNQVGQAIADEMKKRGWKPEEVGALRVTnyelpTAKLRTDGATQAlLA 198
Cdd:cd19968   80 GIPVVTVDRR-AEGA----APVPHVGADNVAGGREVAKFVVDKLPNGAKVIELTGTPGSS-----PAIDRTKGFHEE-LA 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 SGFKKENIFDAPQKTTDDEGG--FSAAAPVLARHPNvkkwVIFALNEETVLGAVRATEQLHIPAADVIGVGINGAGEAFA 276
Cdd:cd19968  149 AGPKIKVVFEQTGNFERDEGLtvMENILTSLPGPPD----AIICANDDMALGAIEAMRAAGLDLKKVKVIGFDAVPDALQ 224

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 309274435 277 EFQKKEptgFFGTIAVSSTNHGKQSAQNLVDWIRSGKAP 315
Cdd:cd19968  225 AIKDGE---LYATVEQPPGGQARTALRILVDYLKDKKAP 260
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
66-329 1.51e-07

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


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 52.12  E-value: 1.51e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  66 QKEGFSVVnIGTPDG--EKVLAAIDNLGSQGAQGFVICAPdvRLGPAIAARAKRYDMKFVTVDDQLVDssgkplANVPHL 143
Cdd:COG1609   88 RERGYQLL-LANSDEdpEREREALRLLLSRRVDGLILAGS--RLDDARLERLAEAGIPVVLIDRPLPD------PGVPSV 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 144 GMSATkignQVGQAIADEMKKRGWKpeEVGALrVTNYELPTAKLRTDGATQALLASG--FKKENIFDAPqktTDDEGGFS 221
Cdd:COG1609  159 GVDNR----AGARLATEHLIELGHR--RIAFI-GGPADSSSARERLAGYREALAEAGlpPDPELVVEGD---FSAESGYE 228

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 222 AAAPVLARHPNVKkwVIFALNEETVLGAVRATEQ--LHIPaADVIGVGINGAgeAFAEFQkkEP--TgffgTIAVSSTNH 297
Cdd:COG1609  229 AARRLLARGPRPT--AIFCANDLMALGALRALREagLRVP-EDVSVVGFDDI--PLARYL--TPplT----TVRQPIEEM 297

                        250       260       270
                 ....*....|....*....|....*....|..
gi 309274435 298 GKQSAQNLVDWIRSGKAPPADTQTSGKLMTRE 329
Cdd:COG1609  298 GRRAAELLLDRIEGPDAPPERVLLPPELVVRE 329
PBP1_ABC_sugar_binding-like cd06317
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; Periplasmic ...
 45-335 3.41e-07

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: 50.84  E-value: 3.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  45 LVKMPEQAWFINE-----QKAATALGQKegfSVVNIGTPDGEKVLAAIDNLGSQGAQGFVICAPDVR-LGPAIAaRAKRY 118
Cdd:cd06317    4 LVQINQQAQFFNQinqgaQAAAKDLGVD---LVVFNANDDPSKQNTAVDNYIARGVDAIILDAIDVNgSIPAIK-RASEA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 119 DMKFVTVDDQLvdSSGKPLANVphlGMSATKIGNQVGQAIADEMKKRGWKPEEVGALRVTNYELPTAklRTDGATQALLA 198
Cdd:cd06317   80 GIPVIAYDAVI--PSDFQAAQV---GVDNLEGGKEIGKYAADYIKAELGGQAKIGVVGALSSLIQNQ--RQKGFEEALKA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 S-GFKKENIFDApqkTTDDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHiPAADVIGVGINGAGEAFae 277
Cdd:cd06317  153 NpGVEIVATVDG---QNVQEKALSAAENLLTANPDLD--AIYATGEPALLGAVAAVRSQG-RQGKIKVFGWDLTKQAI-- 224

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435 278 FQKKEPTGFFGTIAVSSTNHGKQSAQNLVDwIRSGKAPPADTQTSGKLMTRENWQAVR 335
Cdd:cd06317  225 FLGIDEGVLQAVVQQDPEKMGYEAVKAAVK-AIKGEDVEKTIDVPPTIVTKENVDQFR 281
PBP1_ABC_sugar_binding-like cd19971
monosaccharide ABC transporter substrate-binding protein; Periplasmic sugar-binding domain of ...
 79-307 7.45e-07

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: 49.89  E-value: 7.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  79 DGEKVLAAIDNLGSQGAQGFVICAPD---VRlgPAIAArAKRYDMKFVTVDDQLVDSSgkplanvphlgMSATKIGN--- 152
Cdd:cd19971   40 DQNKQNEQIEDMINQGVDAIFLNPVDsegIR--PALEA-AKEAGIPVINVDTPVKDTD-----------LVDSTIASdny 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 153 QVGQAIADEMKKRgwKPEevGAlRVTNYELPTAK---LRTDGATQALlaSGFKKENIFDAPQKTTDDEGGFSAAAPVLAR 229
Cdd:cd19971  106 NAGKLCGEDMVKK--LPE--GA-KIAVLDHPTAEscvDRIDGFLDAI--KKNPKFEVVAQQDGKGQLEVAMPIMEDILQA 178

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435 230 HPNVKkwVIFALNEETVLGAVRATEQLHIPaADVIGVGINGAGEAFAEFQKKEptgFFGTIAVSSTNHGKQSAQNLVD 307
Cdd:cd19971  179 HPDLD--AVFALNDPSALGALAALKAAGKL-GDILVYGVDGSPDAKAAIKDGK---MTATAAQSPIEIGKKAVETAYK 250
PBP1_ribose_binding cd06323
periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose ...
 41-315 2.92e-06

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: 48.06  E-value: 2.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGF-SVVNIGTPDGEKVLAAIDNLGSQGAQGFVICAPDVR-LGPAIAArAKRY 118
Cdd:cd06323    1 TIGLSVSTLNNPFFVSLKDGAQAEAKELGVeLVVLDAQNDPAKQLSQVEDLIVRKVDALLINPTDSDaVSPAVEE-ANEA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 119 DMKFVTVDDQLvdSSGKPLAnvpHLGMSATKIGNQVGQAIADEMKKRGWKPEEVGalrvtnyelptaklrTDGATQAL-L 197
Cdd:cd06323   80 GIPVITVDRSV--TGGKVVS---HIASDNVAGGEMAAEYIAKKLGGKGKVVELQG---------------IPGTSAAReR 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 198 ASGFkkENIFDAPQKTT---------DDEGGFSAAAPVLARHPNVKKwvIFALNEETVLGAVRATEQLHIPaaDVIGVGI 268
Cdd:cd06323  140 GKGF--HNAIAKYPKINvvasqtadfDRTKGLNVMENLLQAHPDIDA--VFAHNDEMALGAIQALKAAGRK--DVIVVGF 213

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 309274435 269 NGAGEAFAEFQKKEptgFFGTIAVSSTNHGKQSAQNLVDWIRSGKAP 315
Cdd:cd06323  214 DGTPDAVKAVKDGK---LAATVAQQPEEMGAKAVETADKYLKGEKVP 257
PBP1_ABC_sugar_binding-like cd06321
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 41-319 5.70e-06

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: 47.28  E-value: 5.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVvNIGTPDGEKVLAA----IDNLGSQGAQGFVICAPD-VRLGPAIAaRA 115
Cdd:cd06321    1 VIGVTVQDLGNPFFVAMVRGAEEAAAEINPGA-KVTVVDARYDLAKqfsqIDDFIAQGVDLILLNAADsAGIEPAIK-RA 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 116 KRYDMKFVTVDdqlvdSSGKPL-ANVphlGMSATKIGNQVGQAIADEMKKRGwkpeEVGALRVTNyeLPTAKLRTDGATQ 194
Cdd:cd06321   79 KDAGIIVVAVD-----VAAEGAdATV---TTDNVQAGYLACEYLVEQLGGKG----KVAIIDGPP--VSAVIDRVNGCKE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 195 ALL-ASGFKkenIFDAPQKTTDDEGGFSAAAPVLARHPNVKKwvIFALNEETVLGAVRATEQLHipAADVIGVGINGAGE 273
Cdd:cd06321  145 ALAeYPGIK---LVDDQNGKGSRAGGLSVMTRMLTAHPDVDG--VFAINDPGAIGALLAAQQAG--RDDIVITSVDGSPE 217

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 309274435 274 AFAEFqKKEPTGFFGTIAVSSTNHGKQSAQNLVDwIRSGKAPPADT 319
Cdd:cd06321  218 AVAAL-KREGSPFIATAAQDPYDMARKAVELALK-ILNGQEPAPEL 261
PBP1_galactofuranose_YtfQ-like cd06309
periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems; ...
 41-330 1.20e-05

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: 46.06  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNI-GTPDGEKVLAAIDNLGSQGAQGFVIcAPDVRLGPAIA-ARAKRY 118
Cdd:cd06309    1 TVGFSQAGSESPWRVANTKSIKEAAKKRGYELVYTdANQDQEKQINDIRDLIAQGVDAILI-SPIDATGWDPVlKEAKDA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 119 DMKFVTVDDQLVDSSGKPLanVPHLGMSATKIGNQVGQAIADEMKKrgwKPEEVGALRVTnYELPTAKLRTDGATQALLA 198
Cdd:cd06309   80 GIPVILVDRTIDGEDGSLY--VTFIGSDFVEEGRRAAEWLVKNYKG---GKGNVVELQGT-AGSSVAIDRSKGFREVIKK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 SGfkkeNIFDAPQKTTD--DEGGFSAAAPVLARHPNvKKWVIFALNEETVLGAVRATEQLHI-PAADVIGVGINGAGEAF 275
Cdd:cd06309  154 HP----NIKIVASQSGNftREKGQKVMENLLQAGPG-DIDVIYAHNDDMALGAIQALKEAGLkPGKDVLVVGIDGQKDAL 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435 276 AEFQKkeptgffGTIAVS---STNHGKQSAQNLVDWIRsGKAPPADTQTSGKLMTREN 330
Cdd:cd06309  229 EAIKA-------GELNATvecNPLFGPTAFDTIAKLLA-GEKVPKLIIVEERLFDKDN 278
PBP1_ABC_sugar_binding-like cd20004
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 41-328 4.73e-05

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: 44.15  E-value: 4.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTPDGEKV---LAAIDNLGSQGAQGFVIcAPDVRlgPAIAARAKR 117
Cdd:cd20004    1 CIAVIPKGTTHDFWKSVKAGAEKAAQELGVEIYWRGPSREDDVeaqIQIIEYFIDQGVDGIVL-APLDR--KALVAPVER 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 118 YDMKFVTVddQLVDSsgkPLANVPHLGMSAT---KIGNQVGQAIADEMKKRGwkpeEVGALRVTNYELPTAKlRTDGATQ 194
Cdd:cd20004   78 ARAQGIPV--VIIDS---DLGGDAVISFVATdnyAAGRLAAKRMAKLLNGKG----KVALLRLAKGSASTTD-RERGFLE 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 195 ALlASGFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKKwvIFALNEETVLGAVRATEQLHIpAADVIGVGINGAGEA 274
Cdd:cd20004  148 AL-KKLAPGLKVVDDQYAGGTVGEARSSAENLLNQYPDVDG--IFTPNESTTIGALRALRRLGL-AGKVKFIGFDASDLL 223

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 309274435 275 FAEFQKKEPTGFfgtIAVSSTNHGKQSAQNLVDWIRsGKAPPADTQTSGKLMTR 328
Cdd:cd20004  224 LDALRAGEISAL---VVQDPYRMGYLGVKTAVAALR-GKPVPKRIDTGVVLVTK 273
PBP1_ABC_xylose_binding-like cd19992
periplasmic xylose-like sugar-binding component of the ABC-type transport systems; Periplasmic ...
 41-164 6.35e-05

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: 44.11  E-value: 6.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSV-VNIGTPDGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYD 119
Cdd:cd19992    1 KIGVSFPTQQEERWQKDKEYMEEEAKELGVELiFQVADNDAKTQASQVENLLAQGIDVLIIAPVDAGAAANIVDKAKAAG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 309274435 120 MKFVTVdDQLVDSSGKPLanvpHLGMSATKIGNQVGQAIADEMKK 164
Cdd:cd19992   81 VPVISY-DRLILNADVDL----YVGRDNYKVGQLQAEYALEAVPK 120
PRK09701 PRK09701
D-allose transporter substrate-binding protein;
66-318 7.95e-05

D-allose transporter substrate-binding protein;


Pssm-ID: 182037 [Multi-domain]  Cd Length: 311  Bit Score: 43.71  E-value: 7.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  66 QKEGFSVVNIGTP---DGEKVLAAIDNLGSQGAQGFVIcAP--DVRLGPAIAaRAKRYDMKFVTVDDQL-VDSSGKPLAN 139
Cdd:PRK09701  51 KTLGVSVDIFASPsegDFQSQLQLFEDLSNKNYKGIAF-APlsSVNLVMPVA-RAWKKGIYLVNLDEKIdMDNLKKAGGN 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 140 VphLGMSAT---KIGNQVGQAIADEMKKRGwkpeevGALRVTNYELPTA--KLRTDGATQALLASGFKKenIFDAPQKTT 214
Cdd:PRK09701 129 V--EAFVTTdnvAVGAKGASFIIDKLGAEG------GEVAIIEGKAGNAsgEARRNGATEAFKKASQIK--LVASQPADW 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 215 DDEGGFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQLHiPAADVIGVGINGAGEAFAEFQKKEPTGffgTIAVSS 294
Cdd:PRK09701 199 DRIKALDVATNVLQRNPNIK--AIYCANDTMAMGVAQAVANAG-KTGKVLVVGTDGIPEARKMVEAGQMTA---TVAQNP 272

                        250       260
                 ....*....|....*....|....
gi 309274435 295 TNHGKQSAQNLVDWIRSGKAPPAD 318
Cdd:PRK09701 273 ADIGATGLKLMVDAEKSGKVIPLD 296
PBP1_ABC_sugar_binding-like cd06310
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 58-255 1.08e-04

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: 43.10  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  58 QKAATALGQKegfsVVNIGTPDGEKVLA---AIDNLGSQGAQGFVICAPDVRLGPAIAARAKRYDMKFVTVDdqlvdSSG 134
Cdd:cd06310   22 EAAAKDLGVK----IIFVGPESEEDVAGqnsLLEELINKKPDAIVVAPLDSEDLVDPLKDAKDKGIPVIVID-----SGI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 135 KPLANVPHLGMSATKIGNQVGQAIADEMKKRGwkpeEVGALRVTNyELPTAKLRTDGATqallaSGFKKE---NIFDAPQ 211
Cdd:cd06310   93 KGDAYLSYIATDNYAAGRLAAQKLAEALGGKG----KVAVLSLTA-GNSTTDQREEGFK-----EYLKKHpggIKVLASQ 162

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 309274435 212 KTTDDEG-GFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQ 255
Cdd:cd06310  163 YAGSDYAkAANETEDLLGKYPDID--GIFATNEITALGAAVAIKS 205
PBP1_ABC_sugar_binding-like cd06324
periplasmic sugar-binding domain of uncharacterized ABC-type transport systems; This group ...
 98-284 2.59e-04

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: 42.21  E-value: 2.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  98 FVICAPDVRLGPAIAARAKRYDMKFVTVDDQLVDSS----GKPLAN----VPHLGMSATKIGNQVGQAIADEMKKRGwKP 169
Cdd:cd06324   61 YLILVNEKGVAPELLELAEQAKIPVFLINNDLTDEErallGKPREKfkywLGSIVPDNEQAGYLLAKALIKAARKKS-DD 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 170 EEVGALRVT-NYELPTAKLRTDGATQAL-LASGFKKENIFDA---PQKttddegGFSAAAPVLARHPNVKkwVIFALNEE 244
Cdd:cd06324  140 GKIRVLAISgDKSTPASILREQGLRDALaEHPDVTLLQIVYAnwsEDE------AYQKTEKLLQRYPDID--IVWAANDA 211

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 309274435 245 TVLGAVRATEQL-HIPAADVIGVGINGAGEAFAEFQKKEPT 284
Cdd:cd06324  212 MALGAIDALEEAgLKPGKDVLVGGIDWSPEALQAVKDGELT 252
PBP1_ABC_sugar_binding-like cd20006
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 86-258 6.97e-04

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: 40.66  E-value: 6.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  86 AIDnlgsQGAQGFVICAPDVRLGPAIAARAKRYDMKFVTVDDQLvdSSGKPLANVphlGMSATKIGNQVGQAIADEMKKR 165
Cdd:cd20006   55 AIA----QKPDAIVLAASDYDRLVEAVERAKKAGIPVITIDSPV--NSKKADSFV---ATDNYEAGKKAGEKLASLLGEK 125

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 166 GwkpeEVGalrVTNYEL--PTAKLRTDGATQALLAsgFKKENIFDAPQKTTDDEGGFSAAAPVLARHPNVKkwVIFALNE 243
Cdd:cd20006  126 G----KVA---IVSFVKgsSTAIEREEGFKQALAE--YPNIKIVETEYCDSDEEKAYEITKELLSKYPDIN--GIVALNE 194

                        170
                 ....*....|....*
gi 309274435 244 ETVLGAVRATEQLHI 258
Cdd:cd20006  195 QSTLGAARALKELGL 209
PBP1_LsrB_Quorum_Sensing-like cd06302
periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium ...
 41-256 7.82e-04

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: 40.69  E-value: 7.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIG--TPDGEKVLAAIDNLGSQGAQGFVICAPDVR-LGPAIaARAKR 117
Cdd:cd06302    1 KIAFVPKVVGIPYFDAAEEGAKKAAKELGVEVVYTGptQADAAQQVQIVENLIAQGVDAIAVSPNDADaLAPVL-KKAKD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 118 YDMKFVTVDDQLVDSSGKPLANvphlGMSATKIGNQVGQAIADEMKKRGWKPEEVGALRVTNYelptaKLRTDGAtQALL 197
Cdd:cd06302   80 AGIKVITWDSDAPPSARDYFVN----QADDEGLGEALVDSLAKEIGGKGKVAILSGSLTATNL-----NAWIKAM-KEYL 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 198 ASGFKKENIFDaPQKTTDDEG-GFSAAAPVLARHPNVKkwVIFALNEETVLGAVRATEQL 256
Cdd:cd06302  150 KSKYPDIELVD-TYYTDDDQQkAYTQAQNLIQAYPDLK--GIIGVSTTAPPAAAQAVEEA 206
PBP1_methylthioribose_binding-like cd06305
similar to methylthioribose-binding protein of ABC-type transport systems that belong to a ...
 41-316 8.51e-04

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: 40.36  E-value: 8.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP-DGEKVLAAIDNLGSQGAQGFVIC-APDVRLGPAIaARAKRY 118
Cdd:cd06305    1 TIAVVRNGTSGDWDQQALQGAVAEAEKLGGTVIVFDANgDDARMADQIQQAITQKVDAIIIShGDADALDPKL-KKALDA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 119 DMKFVTVDdqlVDSSGKPLANVPHLGMSatkIGNQVGQAIADEMKKRGwkpeEVGALRVTNYeLPTAKlRTDGATQALLA 198
Cdd:cd06305   80 GIPVVTFD---TDSQVPGVNNITQDDYA---LGTLSLGQLVKDLNGEG----NIAVFNVFGV-PPLDK-RYDIYKAVLKA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 199 S-GFKKE--NIFDAPQKTTDDEggFSAAAPVLARHPNVKKWVIFALNEETVLGAVRATEQLHipAADVIGVGINGAGEAF 275
Cdd:cd06305  148 NpGIKKIvaELGDVTPNTAADA--QTQVEALLKKYPEGGIDAIWAAWDEPAKGAVQALEEAG--RTDIKVYGVDISNQDL 223

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 309274435 276 AEFQkKEPTGFFGTIAVSSTNHGKQSAQNLVDWIRSGKAPP 316
Cdd:cd06305  224 ELMA-DEGSPWVATAAQDPALIGTVAVRNVARKLAGEDLPD 263
PBP1_ABC_sugar_binding-like cd20008
monosaccharide ABC transporter substrate-binding protein such as CUT2; Periplasmic ...
 41-267 8.64e-04

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: 40.29  E-value: 8.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  41 KIGFLVKMPEQAWFINEQKAATALGQKEGFSVVNIGTP---DGEKVLAAIDNLGSQGAQGFVICAPDVRLGPAIAARAKR 117
Cdd:cd20008    1 KIAVIVKDTDSEYWQTVLKGAEKAAKELGVEVTFLGPAteaDIAGQVNLVENAISRKPDAIVLAPNDTAALVPAVEAADA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 118 yDMKFVtvddqLVDSSGKPLANVPHLGMSATKIGNQVGQAIADEMKKRGWKPEEVGALRVTNYElPTAKLRTDGATQALl 197
Cdd:cd20008   81 -GIPVV-----LVDSGANTDDYDAFLATDNVAAGALAADELAELLKASGGGKGKVAIISFQAGS-QTLVDREEGFRDYI- 152

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 309274435 198 asgfkKENifdAPQKTTDD--------EGGFSAAAPVLARHPNVKKwvIFALNEETVLGAVRATEQlHIPAADVIGVG 267
Cdd:cd20008  153 -----KEK---YPDIEIVDvqysdgdiAKALNQTTDLLTANPDLVG--IFGANNPSAVGVAQALAE-AGKAGKIVLVG 219
PBP1_LacI_sugar_binding-like cd06267
ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 ...
 66-316 1.06e-03

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: 40.19  E-value: 1.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435  66 QKEGFSV-VNIGTPDGEKVLAAIDNLGSQGAQGFVICAPdvRLGPAIAARAKRYDMKFVTVDDQlvdssgkplanVPHLG 144
Cdd:cd06267   26 RERGYSLlLCNTDEDPEREREYLRLLLSRRVDGIILAPS--SLDDELLEELLAAGIPVVLIDRR-----------LDGLG 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 145 MSATKIGN-QVGQAIADEMKKRGWKpeEVGALRvTNYELPTAKLRTDGATQALLASG--FKKENIFDAPqktTDDEGGFS 221
Cdd:cd06267   93 VDSVVVDNyAGAYLATEHLIELGHR--RIAFIG-GPLDLSTSRERLEGYRDALAEAGlpVDPELVVEGD---FSEESGYE 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 309274435 222 AAAPVLARHPNVKkwVIFALNEETVLGAVRATEQ--LHIPaAD--VIGVGingaGEAFAEFQKKEPTgffgTIAVSSTNH 297
Cdd:cd06267  167 AARELLALPPRPT--AIFAANDLMAIGALRALRElgLRVP-EDisVVGFD----DIPLAALLTPPLT----TVRQPAYEM 235

                        250
                 ....*....|....*....
gi 309274435 298 GKQSAQNLVDWIRSGKAPP 316
Cdd:cd06267  236 GRAAAELLLERIEGEEEPP 254
 
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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