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Conserved domains on  [gi|1781386671|gb|QGT51252|]
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hypothetical protein Firmicute1046_3280 [uncultured Firmicutes bacterium]

Protein Classification

type 2 periplasmic-binding domain-containing protein( domain architecture ID 229383)

type 2 periplasmic-binding protein (PBP2) is typically comprised of two globular subdomains connected by a flexible hinge; it binds its ligand in the cleft between these domains in a manner resembling a Venus flytrap; similar to the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Periplasmic_Binding_Protein_Type_2 super family cl21456
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 42-514 1.83e-73

Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences.


The actual alignment was detected with superfamily member cd13583:

Pssm-ID: 473866 [Multi-domain]  Cd Length: 478  Bit Score: 241.11  E-value: 1.83e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  42 PISIDMMLLNNTSGDGAE--FVFKELvKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALV 119
Cdd:cd13583     1 PLTLSMMYRDHPNYPVKDdwLIWKEI-EEKTNVKFKRTPIPSSDYETKRSLLIASGDAPDIIPVLYPGEENEFVASGALL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 120 AVDEYFDYLPNFVKYLEEDETNKI--SAMADDGHIYALPRFAVGKT-DYKWTpiIRQDYLEELNIPVPTTYKELFDALRK 196
Cdd:cd13583    80 PISDYLDYMPNYKKYVEKWGLGKElaTGRQSDGKYYSLPGLHEDPGvQYSFL--YRKDIFEKAGIKIPTTWDEFYAALKK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 197 IKAAHPDTVGIVNREK------MTFLKAFGVGYNTYDTMFYNKENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFTA 270
Cdd:cd13583   158 LKEKYPDSYPYSDRWNsnalllIAAPAFGTTAGWGFSNYTYDPDTDKFVYGATTDEYKDMLQYFNKLYAEGLLDPESFTQ 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 271 SEQQWQEKFLNGSGVFTLDWPkrAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYtqkrlNYSETLGLWTSWGISAN---T 347
Cdd:cd13583   238 TDDQAKAKFLNGKSFVITTNP--QTVDELQRNLRAADGGNYEVVSITPPAGPAG-----KAINGSRLENGFMISSKakdS 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 348 KHLGRILQMVDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMNTLGLNHNRIMRVEKDNGVVEV 427
Cdd:cd13583   311 KNFEALLQFLDWLYSDEGQELATWGVEGETYTKEGDGKVYLADSNTPALNPSGTKLLQKDFGFSDGVFTDGGGTSGKLSE 390

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 428 PEALNKIIQgyrDNVEGYETDY--KIALTFTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSEFDSFVGQIKQQGGSE 505
Cdd:cd13583   391 MTPEEAEFN---DTMLENRKPVppIPPPPMTEEELEQLSLLETPLKDFVDEMTAKFITGKRSMDEWDAFVAEVKKLGLDQ 467


                  ....*....
gi 1781386671 506 LEEIYASAY 514
Cdd:cd13583   468 LLDIYNDAY 476
 
Name Accession Description Interval E-value
PBP2_AlgQ_like_4 cd13583
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 42-514 1.83e-73

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270301 [Multi-domain]  Cd Length: 478  Bit Score: 241.11  E-value: 1.83e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  42 PISIDMMLLNNTSGDGAE--FVFKELvKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALV 119
Cdd:cd13583     1 PLTLSMMYRDHPNYPVKDdwLIWKEI-EEKTNVKFKRTPIPSSDYETKRSLLIASGDAPDIIPVLYPGEENEFVASGALL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 120 AVDEYFDYLPNFVKYLEEDETNKI--SAMADDGHIYALPRFAVGKT-DYKWTpiIRQDYLEELNIPVPTTYKELFDALRK 196
Cdd:cd13583    80 PISDYLDYMPNYKKYVEKWGLGKElaTGRQSDGKYYSLPGLHEDPGvQYSFL--YRKDIFEKAGIKIPTTWDEFYAALKK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 197 IKAAHPDTVGIVNREK------MTFLKAFGVGYNTYDTMFYNKENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFTA 270
Cdd:cd13583   158 LKEKYPDSYPYSDRWNsnalllIAAPAFGTTAGWGFSNYTYDPDTDKFVYGATTDEYKDMLQYFNKLYAEGLLDPESFTQ 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 271 SEQQWQEKFLNGSGVFTLDWPkrAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYtqkrlNYSETLGLWTSWGISAN---T 347
Cdd:cd13583   238 TDDQAKAKFLNGKSFVITTNP--QTVDELQRNLRAADGGNYEVVSITPPAGPAG-----KAINGSRLENGFMISSKakdS 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 348 KHLGRILQMVDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMNTLGLNHNRIMRVEKDNGVVEV 427
Cdd:cd13583   311 KNFEALLQFLDWLYSDEGQELATWGVEGETYTKEGDGKVYLADSNTPALNPSGTKLLQKDFGFSDGVFTDGGGTSGKLSE 390

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 428 PEALNKIIQgyrDNVEGYETDY--KIALTFTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSEFDSFVGQIKQQGGSE 505
Cdd:cd13583   391 MTPEEAEFN---DTMLENRKPVppIPPPPMTEEELEQLSLLETPLKDFVDEMTAKFITGKRSMDEWDAFVAEVKKLGLDQ 467


                  ....*....
gi 1781386671 506 LEEIYASAY 514
Cdd:cd13583   468 LLDIYNDAY 476
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 13-370 1.12e-27

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 113.99  E-value: 1.12e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  13 SMAAVLTTSLLAGCGKGADDISADmdtSTPISIDMMLLNNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLI 92
Cdd:COG1653     6 LALAAALALALAACGGGGSGAAAA---AGKVTLTVWHTGGGEAAALEALIKEFEAEHPGIKVEVESVPYDDYRTKLLTAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  93 ASNELPDIVSpLPADRTKLIGPKGALVAVDEYF--------DYLPNFVKYleedetnkisaMADDGHIYALPRFAvgktd 164
Cdd:COG1653    83 AAGNAPDVVQ-VDSGWLAEFAAAGALVPLDDLLdddgldkdDFLPGALDA-----------GTYDGKLYGVPFNT----- 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 165 ykWTPII--RQDYLEELNIPVPTTYKELFDALRKIKAAHPDTvGIVNREK-----MTFLKAFGVGYntYDtmfynkENDK 237
Cdd:COG1653   146 --DTLGLyyNKDLFEKAGLDPPKTWDELLAAAKKLKAKDGVY-GFALGGKdgaawLDLLLSAGGDL--YD------EDGK 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 238 FEFGpmNSGFKEMITDFAQAWQDGVLDKEFFTASEQQWQEKFLNGSGVFTLDWPkraytlkDSYQKLNPNDTKFNTNLID 317
Cdd:COG1653   215 PAFD--SPEAVEALEFLKDLVKDGYVPPGALGTDWDDARAAFASGKAAMMINGS-------WALGALKDAAPDFDVGVAP 285

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1781386671 318 -PLVSEGYTQkrlnySETLGLWtSWGISANTKHLGRILQMVDWAYSEEAQNEIQ 370
Cdd:COG1653   286 lPGGPGGKKP-----ASVLGGS-GLAIPKGSKNPEAAWKFLKFLTSPEAQAKWD 333
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 51-366 6.52e-13

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 69.37  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  51 NNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALVAVDEYFDylpn 130
Cdd:pfam01547   3 SLTEAAALQALVKEFEKEHPGIKVEVESVGSGSLAQKLTTAIAAGDGPADVFASDNDWIAELAKAGLLLPLDDYVA---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 131 fvKYLEEDetnkisamadDGHIYALPRFAVGktdykWTPIIRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIVNR 210
Cdd:pfam01547  79 --NYLVLG----------VPKLYGVPLAAET-----LGLIYNKDLFKKAGLDPPKTWDELLEAAKKLKEKGKSPGGAGGG 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 211 EKMTFLKAFgvgYNTYDTMFYNKENDKFEFGPMNSGFKEMIT-----DFAQAWQDGVLDKEFFTASEQQWQEKFLNGSGV 285
Cdd:pfam01547 142 DASGTLGYF---TLALLASLGGPLFDKDGGGLDNPEAVDAITyyvdlYAKVLLLKKLKNPGVAGADGREALALFEQGKAA 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 286 FTLDWPKRAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYTQKRLNYSETlglwtsWGISANTKHLGRILQMVDWAYSEEA 365
Cdd:pfam01547 219 MGIVGPWAALAANKVKLKVAFAAPAPDPKGDVGYAPLPAGKGGKGGGYG------LAIPKGSKNKEAAKKFLDFLTSPEA 292


                  .
gi 1781386671 366 Q 366
Cdd:pfam01547 293 Q 293
 
Name Accession Description Interval E-value
PBP2_AlgQ_like_4 cd13583
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 42-514 1.83e-73

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270301 [Multi-domain]  Cd Length: 478  Bit Score: 241.11  E-value: 1.83e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  42 PISIDMMLLNNTSGDGAE--FVFKELvKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALV 119
Cdd:cd13583     1 PLTLSMMYRDHPNYPVKDdwLIWKEI-EEKTNVKFKRTPIPSSDYETKRSLLIASGDAPDIIPVLYPGEENEFVASGALL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 120 AVDEYFDYLPNFVKYLEEDETNKI--SAMADDGHIYALPRFAVGKT-DYKWTpiIRQDYLEELNIPVPTTYKELFDALRK 196
Cdd:cd13583    80 PISDYLDYMPNYKKYVEKWGLGKElaTGRQSDGKYYSLPGLHEDPGvQYSFL--YRKDIFEKAGIKIPTTWDEFYAALKK 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 197 IKAAHPDTVGIVNREK------MTFLKAFGVGYNTYDTMFYNKENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFTA 270
Cdd:cd13583   158 LKEKYPDSYPYSDRWNsnalllIAAPAFGTTAGWGFSNYTYDPDTDKFVYGATTDEYKDMLQYFNKLYAEGLLDPESFTQ 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 271 SEQQWQEKFLNGSGVFTLDWPkrAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYtqkrlNYSETLGLWTSWGISAN---T 347
Cdd:cd13583   238 TDDQAKAKFLNGKSFVITTNP--QTVDELQRNLRAADGGNYEVVSITPPAGPAG-----KAINGSRLENGFMISSKakdS 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 348 KHLGRILQMVDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMNTLGLNHNRIMRVEKDNGVVEV 427
Cdd:cd13583   311 KNFEALLQFLDWLYSDEGQELATWGVEGETYTKEGDGKVYLADSNTPALNPSGTKLLQKDFGFSDGVFTDGGGTSGKLSE 390

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 428 PEALNKIIQgyrDNVEGYETDY--KIALTFTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSEFDSFVGQIKQQGGSE 505
Cdd:cd13583   391 MTPEEAEFN---DTMLENRKPVppIPPPPMTEEELEQLSLLETPLKDFVDEMTAKFITGKRSMDEWDAFVAEVKKLGLDQ 467


                  ....*....
gi 1781386671 506 LEEIYASAY 514
Cdd:cd13583   468 LLDIYNDAY 476
PBP2_AlgQ_like_1 cd13580
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 41-516 7.81e-60

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270298 [Multi-domain]  Cd Length: 471  Bit Score: 204.87  E-value: 7.81e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  41 TPISIDMM--LLNNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGAL 118
Cdd:cd13580     1 EPVTITIVanLGGNPKPDPDDNPYTKYLEEKTNIDVKVKWVPDSSYDEKLNLALASGDLPDIVVVNDPQLSITLVKQGAL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 119 VAVDEYFD-YLPNFVKYLEEDetNKISAMaDDGHIYALPRFAVGKTDYkwTPIIRQDYLEELNIPVPTTYKELFDALRKI 197
Cdd:cd13580    81 WDLTDYLDkYYPNLKKIIEQE--GWDSAS-VDGKIYGIPRKRPLIGRN--GLWIRKDWLDKLGLEVPKTLDELYEVAKAF 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 198 KAAHPD------TVGIVNREKMT--FLKAFGVGYNTYDTMFYNKENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFT 269
Cdd:cd13580   156 TEKDPDgngkkdTYGLTDTKDLIgsGFTGLFGAFGAPPNNWWKDEDGKLVPGSIQPEMKEALKFLKKLYKEGLIDPEFAV 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 270 ASEQQWQEKFLNG-SGVFTLDWPkRAYTLKDSYQKLNPNDtkfNTNLIDPLVSEGytqKRLNYSETLGLWTSWGISANTK 348
Cdd:cd13580   236 NDGTKANEKFISGkAGIFVGNWW-DPAWPQASLKKNDPDA---EWVAVPIPSGPD---GKYGVWAESGVNGFFVIPKKSK 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 349 HLGRILQMVDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMNTLGLNHNRIMRV-EKDNGVVEV 427
Cdd:cd13580   309 KPEAILKLLDFLSDPEVQKLLDYGIEGVHYTVKDGGPVNIIPPDKQEVGDATLDYFQGSLALEKYKLTNNgERKSDAKKE 388

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 428 PEALNKIIQGYRDNVEGYETDYkialtfTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSEFDSFVGQIKQQGGSELE 507
Cdd:cd13580   389 ALDERVVNANDEENENIAVGPP------TETLVSPTEKYGATLDKLEDDAFTKIIMGQIPLDEFDKFVEEWKKSGGDEIT 462


                  ....*....
gi 1781386671 508 EIYASAYAS 516
Cdd:cd13580   463 KEVNEWYKE 471
PBP2_AlgQ1_2 cd13584
Periplasmic-binding component of alginate-specific ABC uptake system; contains the type 2 ...
 61-515 2.39e-52

Periplasmic-binding component of alginate-specific ABC uptake system; contains the type 2 periplasmic binding fold; This group represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria such as Sphingomonas sp. A1. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that includes alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270302 [Multi-domain]  Cd Length: 481  Bit Score: 184.95  E-value: 2.39e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  61 VFKELVKeKFNIDIKFSLNN-NQSHFEKLNLLIASNELPDIVSPLPADRTKLI---GPKGALVAVDEYFD-YLPNFVKYL 135
Cdd:cd13584    22 VYKEMER-KTNVKLNFVANPvAQNSQEQFNLMMASGQLPDIIGGDWLKDKGGFekyGEDGAFLPLNDLIDqYAPNLKKFL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 136 EEDETNKISAMADDGHIYALPRFAVGKTDYKWT-PIIRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIVNREKMT 214
Cdd:cd13584   101 DEHPDVKKAITTDDGNIYGFPYLPDGDVAKEARgYFIRKDWLDKLGLKTPSTIDEWYTVLKAFKERDPNGNGKADEVPLI 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 215 FLK-----------AFGVgyntyDTMFYNKENDKFeFGPMNSGFKEMITDFAQAWQDGVLDKEFFTASEQQWQEKFLNG- 282
Cdd:cd13584   181 LTKpgydetgrlinAWGA-----YMDFYQENGKVK-YGPLEPGFKDFLKTMNQWYKEGLIDPDFFTRKAKAREQNIMNGn 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 283 SGVFTLDWpkrAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYTQKRLNYSETLGLWTSWGISANTKHLGRILQMVDWAYS 362
Cdd:cd13584   255 IGGFTHDW---FASTGTFNLALLKNVPDFKLVAVPPPVLNKGQTPYEEDSRQIAKGDGAAITASNKNPVLAIKWLDYAYS 331

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 363 EEAQNEIQWGLEGKHYTVnEDGRYQYTPEMKASYNPegtvdPMNTLGLNhnriMRVEKDNGVVEVPEALNK-IIQGYRDN 441
Cdd:cd13584   332 EEGRLLSNFGVEGESYTI-KNGKPVFTDDVLKDPQP-----LVNALSLY----YGAQIPGGFWQDYEYEEQwTTPEALES 401

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1781386671 442 VEGYETD----YKIALTFTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSE-FDSFVGQIKQQGGSELEEIYASAYA 515
Cdd:cd13584   402 KDIYAKNkyvmPLPPVTLTEEERSIYDSIMTDIDTYVNEMGQKWIMGKEDADDnWDEYQKKLKSLGLYEALEIQQAAYD 480
PBP2_AlgQ_like cd13521
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 47-515 1.50e-47

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This family represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria and related proteins. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. In Sphingomonas sp. A1, the transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270239 [Multi-domain]  Cd Length: 483  Bit Score: 171.87  E-value: 1.50e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  47 MMLLNNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIV-SPLPADRTKLIGPKGALVAVDEYF 125
Cdd:cd13521     7 LMAFNDNWVDDENWPVAKEIEKLTNVKLEIVAVTAATSQQKLNLMLASGDLPDIVgADYLKDKFIAYGMEGAFLPLSKYI 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 126 DYLPNFVKYLEEDETNKISAMADDGHIYALPRFAVGKTdYKWTPIIRQDYLEELNIPVPTTYKELFDALRKIKAAHP--- 202
Cdd:cd13521    87 DQYPNLKAFFKQHPDVLRASTASDGKIYLIPYEPPKDV-PNQGYFIRKDWLDKLNLKTPKTLDELYNVLKAFKEKDPngn 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 203 ---DTVGIVNREKM----------TFLKAFGVGYNTYDTmfynkENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFT 269
Cdd:cd13521   166 gkaDEIPFIDRDPLygafrlinswGARSAGGSTDSDWYE-----DNGKFKHPFASEEYKDGMKYMNKLYTEGLIDKESFT 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 270 ASEQQWQEKFLNG-SGVFTLDW-----PKRAYTLKDSYQKLnpndtkfntnLIDPLVSEGYTQKRLNYSETLGLWTSWGI 343
Cdd:cd13521   241 QKDDQAEQKFSNGkLGGFTHNWfasdnLFTAQLGKEKPMYI----------LLPIAPAGNVKGRREEDSPGYTGPDGVAI 310

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 344 SANTKHLGRILQMVDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKAsynpEGTVD-PMNTLGlnhNRIMRVEKDN 422
Cdd:cd13521   311 SKKAKNPVAALKFFDWLASEEGRELANFGIEGVHYNKDNGKKRTKDPVKKS----DQPGDnQLYDLP---AFIKGGFWNE 383

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 423 GVVEVPEALNKIIQGYRDNVEGYETDYKIALTF-----TEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPM-SEFDSFVG 496
Cdd:cd13521   384 YTYPRPQWGVLTGDSARLPIDMYIKPKYSPPKPeganlTIEEREQVSIDNTELKDIMMEMTQKWIMGTKEKdEEWDAYQE 463

                         490
                  ....*....|....*....
gi 1781386671 497 QIKQQGGSELEEIYASAYA 515
Cdd:cd13521   464 QLKSAGLYQVTEEVQKAYD 482
PBP2_AlgQ_like_2 cd13581
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 61-515 3.80e-42

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270299 [Multi-domain]  Cd Length: 490  Bit Score: 157.10  E-value: 3.80e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  61 VFKELvKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIV--SPLPADRTKLIGPKGALVAVDEYFD-YLPNFVKYLEE 137
Cdd:cd13581    22 FFKRL-EEKTGIKIEWETVPEDAWAEKKNLMLASGDLPDAFlgAGASDADLMTYGKQGLFLPLEDLIDkYAPNLKALFDE 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 138 DETNKISAMADDGHIYALPR-FAVGKTDYKWTPIIRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIVNREKMTFL 216
Cdd:cd13581   101 NPDIKAAITAPDGHIYALPSvNECYHCSYGQRMWINKKWLDKLGLEMPTTTDELYEVLKAFKEQDPNGNGKADEIPLSFS 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 217 K-------------AFGVGYNTYDTMFYNKENDKFEFGPMNSGFKEMITDFAQAWQDGVLDKEFFTASEQQWQEKFLNGS 283
Cdd:cd13581   181 GlnggtddpafllnSFGINDGGYGGYGFVVKDGKVIYTATDPEYKEALAYLNKLYKEGLIDPEAFTQDYDQLAAKGKAST 260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 284 ---GVFTLdWPKRAYTLKDSYQKLNPndtkfntnlIDPLVSEG--YTQKRLNYSEtlglWTSWG--ISANTKHLGRILQM 356
Cdd:cd13581   261 akvGVFFG-WDPGLFFGEERYEQYVP---------LPPLKGPNgdQLAWVGNSSG----YGRGGfvITSKNKNPEAAIRW 326

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 357 VDWAYSEEAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMN-TLGLNHNRIMRVEKDNGVVEVPEALNKII 435
Cdd:cd13581   327 ADFLYSPEGSLQANFGPEGEDWEKNPDGEYGVDGPPAAYKILEPSEGEQNvAWADGGPGAIPDEYRLKQVTDEDMDEAEA 406

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 436 QGYR--DNVEGYE-TDYKIALTFTEEQSDRIEEIKMVTDTLVNEGVVAFVTGTRPMSEFDSFVGQIKQQGGSELEEIYAS 512
Cdd:cd13581   407 RLDEakKYYEPYApPDNSPPPALLDEEAEKISTIQTDINNYIEQKRAKFITGGGDDKEWDAYVKQLEKMGLDEYLEIYQK 486


                  ...
gi 1781386671 513 AYA 515
Cdd:cd13581   487 AYD 489
PBP2_AlgQ_like_3 cd13582
Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 ...
 61-397 2.61e-36

Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold; This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide.


Pssm-ID: 270300 [Multi-domain]  Cd Length: 504  Bit Score: 141.30  E-value: 2.61e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  61 VFKELVKE-KFNIDIKFSLNNNQshfEKLNLLIASNELPDIVSPlPADRTKLIGpKGALVAVDEYFD-YLPNfVKYLEED 138
Cdd:cd13582    22 VAKKITELtGVTLEIEYLVGGEK---QKIGLMIASGDLPDLIYA-KGDTDKLIE-AGALVPLDDLIEkYGPN-IKKWYGD 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 139 ETNKISAmADDGHIYALPRFavGKTDYKWTP----IIRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVG-------- 206
Cdd:cd13582    96 YLLKKLR-SEDGHIYYLPNY--RVEDAPWYPnggfWLQHDVLKELGYPKIKTLDDYENLIKDYKKKYPTINGqptigfta 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 207 IVNREKMTFLKAFGVGYNTY-DTMFYNKENDKFE--FGPMNSGFKEMITDFAQAWQDGVLDKEFFTASEQQWQEKFLNGS 283
Cdd:cd13582   173 LTDDWRFLISVTNPAFLAGYpNDGEVYVDPKTLKakFHYTRPYYKEYYKWLNELWNEGLLDKESFTQKYDQYLAKIASGR 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 284 GVFTLDwpkRAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYTQKRLNYSETLGLWTSWGISANTKHLGRILQMVDWAYSE 363
Cdd:cd13582   253 VLGFYD---AGWDIGNAITALKAKGKDERLYAYYPVAVGVDDKDYNYGDPGYLGGDGIAITKSCKDPERAFKFLDWLASE 329

                         330       340       350
                  ....*....|....*....|....*....|....
gi 1781386671 364 EAQNEIQWGLEGKHYTVNEDGRYQYTPEMKASYN 397
Cdd:cd13582   330 EAQKLINWGIEGVDYDVDDGKRVYLTEEMAAKNK 363
UgpB COG1653
ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport ...
 13-370 1.12e-27

ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism];


Pssm-ID: 441259 [Multi-domain]  Cd Length: 363  Bit Score: 113.99  E-value: 1.12e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  13 SMAAVLTTSLLAGCGKGADDISADmdtSTPISIDMMLLNNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLI 92
Cdd:COG1653     6 LALAAALALALAACGGGGSGAAAA---AGKVTLTVWHTGGGEAAALEALIKEFEAEHPGIKVEVESVPYDDYRTKLLTAL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  93 ASNELPDIVSpLPADRTKLIGPKGALVAVDEYF--------DYLPNFVKYleedetnkisaMADDGHIYALPRFAvgktd 164
Cdd:COG1653    83 AAGNAPDVVQ-VDSGWLAEFAAAGALVPLDDLLdddgldkdDFLPGALDA-----------GTYDGKLYGVPFNT----- 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 165 ykWTPII--RQDYLEELNIPVPTTYKELFDALRKIKAAHPDTvGIVNREK-----MTFLKAFGVGYntYDtmfynkENDK 237
Cdd:COG1653   146 --DTLGLyyNKDLFEKAGLDPPKTWDELLAAAKKLKAKDGVY-GFALGGKdgaawLDLLLSAGGDL--YD------EDGK 214

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 238 FEFGpmNSGFKEMITDFAQAWQDGVLDKEFFTASEQQWQEKFLNGSGVFTLDWPkraytlkDSYQKLNPNDTKFNTNLID 317
Cdd:COG1653   215 PAFD--SPEAVEALEFLKDLVKDGYVPPGALGTDWDDARAAFASGKAAMMINGS-------WALGALKDAAPDFDVGVAP 285

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1781386671 318 -PLVSEGYTQkrlnySETLGLWtSWGISANTKHLGRILQMVDWAYSEEAQNEIQ 370
Cdd:COG1653   286 lPGGPGGKKP-----ASVLGGS-GLAIPKGSKNPEAAWKFLKFLTSPEAQAKWD 333
PBP2_TMBP_like cd13585
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and ...
 61-407 1.81e-15

The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold; This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270303 [Multi-domain]  Cd Length: 383  Bit Score: 78.22  E-value: 1.81e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  61 VFKELVK--EKFNIDIKFSL--NNNQSHFEKLNLLIASNELPDIVSpLPADRTKLIGPKGALVAVDEYFDYLPNFVKYLE 136
Cdd:cd13585    15 ALKKLIDafEKENPGVKVEVvpVPYDDYWTKLTTAAAAGTAPDVFY-VDGPWVPEFASNGALLDLDDYIEKDGLDDDFPP 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 137 edetNKISAMADDGHIYALPrfavgktdYKWTPII---RQDYLEE--LNIPVPTTYKELFDALRKIKAAHPDTVGIVNRE 211
Cdd:cd13585    94 ----GLLDAGTYDGKLYGLP--------FDADTLVlfyNKDLFDKagPGPKPPWTWDELLEAAKKLTDKKGGQYGFALRG 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 212 K-------MTFLKAFGvgyntydTMFYNKENDKFEFgpmNS-GFKEMITDFAQAWQDGVLDKEFfTASEQQWQEKFLNGS 283
Cdd:cd13585   162 GsggqtqwYPFLWSNG-------GDLLDEDDGKATL---NSpEAVEALQFYVDLYKDGVAPSSA-TTGGDEAVDLFASGK 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 284 GVFTLDWPKRAYTLKDSyqklnpnDTKFNTNLIDPLVSEGYTQKrlnyseTLGLWTSWGISANTKHLGRILQMVDWAYSE 363
Cdd:cd13585   231 VAMMIDGPWALGTLKDS-------KVKFKWGVAPLPAGPGGKRA------SVLGGWGLAISKNSKHPEAAWKFIKFLTSK 297

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 1781386671 364 EAQneIQWGLEGKHYTVNEDGRYQYTPEMKASYNPEGTVDPMNT 407
Cdd:cd13585   298 ENQ--LKLGGAAGPAALAAAAASAAAPDAKPALALAAAADALAA 339
MalE COG2182
Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];
2-366 1.26e-13

Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism];


Pssm-ID: 441785 [Multi-domain]  Cd Length: 410  Bit Score: 72.67  E-value: 1.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671   2 MKqiwKKVIGFSMAAVLTTSLLAGCGKGADDISADMDTSTPISIdMMLLNNTSGDGAEFVFKElVKEKFNIDIKFSLNNN 81
Cdd:COG2182     1 MK---RRLLAALALALALALALAACGSGSSSSGSSSAAGAGGTL-TVWVDDDEAEALEEAAAA-FEEEPGIKVKVVEVPW 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  82 QSHFEKLNLLIASNELPDIVSpLPADRtklIGP---KGALVAVDEYFDYLPNFVKYLeedetnkISAMADDGHIYALPrF 158
Cdd:COG2182    76 DDLREKLTTAAPAGKGPDVFV-GAHDW---LGElaeAGLLAPLDDDLADKDDFLPAA-------LDAVTYDGKLYGVP-Y 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 159 AVgKTdykWTPIIRQDYLEElniPVPTTYKELFDALRKIKAAhpDTVGIVNREK-----MTFLKAFGvGYntydtMFYNK 233
Cdd:COG2182   144 AV-ET---LALYYNKDLVKA---EPPKTWDELIAAAKKLTAA--GKYGLAYDAGdayyfYPFLAAFG-GY-----LFGKD 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 234 ENDKFEFGpMNSgfKEMItDFAQAWQD----GVLDKEfftASEQQWQEKFLNGSGVFTLDWPKRAYTLKDSYqklnpndt 309
Cdd:COG2182   209 GDDPKDVG-LNS--PGAV-AALEYLKDlikdGVLPAD---ADYDAADALFAEGKAAMIINGPWAAADLKKAL-------- 273

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 310 kfNTNL-IDPL--VSEGYTQKRLnysetLGLWtSWGISANTKHLGRILQMVDWAYSEEAQ 366
Cdd:COG2182   274 --GIDYgVAPLptLAGGKPAKPF-----VGVK-GFGVSAYSKNKEAAQEFAEYLTSPEAQ 325
SBP_bac_1 pfam01547
Bacterial extracellular solute-binding protein; This family also includes the bacterial ...
 51-366 6.52e-13

Bacterial extracellular solute-binding protein; This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.


Pssm-ID: 460248 [Multi-domain]  Cd Length: 294  Bit Score: 69.37  E-value: 6.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  51 NNTSGDGAEFVFKELVKEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALVAVDEYFDylpn 130
Cdd:pfam01547   3 SLTEAAALQALVKEFEKEHPGIKVEVESVGSGSLAQKLTTAIAAGDGPADVFASDNDWIAELAKAGLLLPLDDYVA---- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 131 fvKYLEEDetnkisamadDGHIYALPRFAVGktdykWTPIIRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIVNR 210
Cdd:pfam01547  79 --NYLVLG----------VPKLYGVPLAAET-----LGLIYNKDLFKKAGLDPPKTWDELLEAAKKLKEKGKSPGGAGGG 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 211 EKMTFLKAFgvgYNTYDTMFYNKENDKFEFGPMNSGFKEMIT-----DFAQAWQDGVLDKEFFTASEQQWQEKFLNGSGV 285
Cdd:pfam01547 142 DASGTLGYF---TLALLASLGGPLFDKDGGGLDNPEAVDAITyyvdlYAKVLLLKKLKNPGVAGADGREALALFEQGKAA 218

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 286 FTLDWPKRAYTLKDSYQKLNPNDTKFNTNLIDPLVSEGYTQKRLNYSETlglwtsWGISANTKHLGRILQMVDWAYSEEA 365
Cdd:pfam01547 219 MGIVGPWAALAANKVKLKVAFAAPAPDPKGDVGYAPLPAGKGGKGGGYG------LAIPKGSKNKEAAKKFLDFLTSPEA 292


                  .
gi 1781386671 366 Q 366
Cdd:pfam01547 293 Q 293
PBP2_TMBP cd14750
The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; ...
 67-383 1.83e-07

The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold; This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270453 [Multi-domain]  Cd Length: 385  Bit Score: 53.45  E-value: 1.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  67 KEKFNIDIKF---SLNNNQSHFEKLNLLIASNELPDIVS------PLPADRTkLIGPKGALVAVDEYFDYLPNFVKylee 137
Cdd:cd14750    25 KKHPDIKVEIeelPASSDDQRQQLVTALAAGSSAPDVLGldviwiPEFAEAG-WLLPLTEYLKEEEDDDFLPATVE---- 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 138 detnkisAMADDGHIYALPRFA-VGKTDYkwtpiiRQDYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIVNREK---- 212
Cdd:cd14750   100 -------ANTYDGKLYALPWFTdAGLLYY------RKDLLEKYGPEPPKTWDELLEAAKKRKAGEPGIWGYVFQGKqyeg 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 213 -----MTFLKAFGVGyntydtmFYNKENDKFEFGPmnsgfKEMIT--DFAQAW-QDGVLDKEFFTASEQQWQEKFLNGSG 284
Cdd:cd14750   167 lvcnfLELLWSNGGD-------IFDDDSGKVTVDS-----PEALEalQFLRDLiGEGISPKGVLTYGEEEARAAFQAGKA 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 285 VFTLDWPKrAYTLKDSYQKLNPNDTKFNTnliDPLVSEGYTqkrlnySETLGLWTsWGISANTKHLGRILQMVDWAYSEE 364
Cdd:cd14750   235 AFMRNWPY-AYALLQGPESAVAGKVGVAP---LPAGPGGGS------ASTLGGWN-LAISANSKHKEAAWEFVKFLTSPE 303

                         330
                  ....*....|....*....
gi 1781386671 365 AQneIQWGLEGKHYTVNED 383
Cdd:cd14750   304 VQ--KRRAINGGLPPTRRA 320
PBP2_UgpB cd14748
The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; ...
 51-291 1.60e-06

The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold; This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270451 [Multi-domain]  Cd Length: 385  Bit Score: 50.37  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  51 NNTSGDGAefVFKELVKEkFN-----IDIKFSLNNNQSHFE-KLNLLIASNELPDIVSpLPADRTKLIGPKGALVAVDEY 124
Cdd:cd14748     7 GMSGPDGK--ALEELVDE-FNkshpdIKVKAVYQGSYDDTLtKLLAALAAGTAPDVAQ-VDASWVAQLADSGALEPLDDY 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 125 F--------DYLPNFVKYLEEDetnkisamaddGHIYALPrFAVgktdykWTPII--RQDYLEE--LNIP-VPTTYKELF 191
Cdd:cd14748    83 IdkdgvdddDFYPAALDAGTYD-----------GKLYGLP-FDT------STPVLyyNKDLFEEagLDPEkPPKTWDELE 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 192 DALRKIKAAhpdtvgIVNREKMTFLKAFGVGYNTYDTM-------FYNKENDKFEFgpmNSgfKEMItDFAQAWQDGVLD 264
Cdd:cd14748   145 EAAKKLKDK------GGKTGRYGFALPPGDGGWTFQALlwqnggdLLDEDGGKVTF---NS--PEGV-EALEFLVDLVGK 212

                         250       260
                  ....*....|....*....|....*...
gi 1781386671 265 KEFFTASEQQWQEK-FLNGSGVFTLDWP 291
Cdd:cd14748   213 DGVSPLNDWGDAQDaFISGKVAMTINGT 240
SBP_bac_8 pfam13416
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ...
 67-368 1.72e-06

Bacterial extracellular solute-binding protein; This family includes bacterial extracellular solute-binding proteins.


Pssm-ID: 433189 [Multi-domain]  Cd Length: 281  Bit Score: 49.71  E-value: 1.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  67 KEKFNIDIKFSLNNNQSHFEKLNLLIASNELPDI-VSPLPADRTKLIGPKGALVAVDEYFDYlpnfvkyleEDETNKISA 145
Cdd:pfam13416   7 EKKTGVTVEVEPQASNDLQAKLLAAAAAGNAPDLdVVWIAADQLATLAEAGLLADLSDVDNL---------DDLPDALDA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 146 MADDGHIYALPrFAVGKTDykwTPIIRQDYLEElNIPVPTTYKELFDALRKIKAAhpdtVGIVNRekmtflkafgvGYNT 225
Cdd:pfam13416  78 AGYDGKLYGVP-YAASTPT---VLYYNKDLLKK-AGEDPKTWDELLAAAAKLKGK----TGLTDP-----------ATGW 137

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 226 YDTMFYNKENDKFEFGPMNSGFKEmitdfAQAWQDGVLDKEFFTASEQQWQEKFLNGSGVFTLDWPKRAYTLKDSYQKLN 305
Cdd:pfam13416 138 LLWALLADGVDLTDDGKGVEALDE-----ALAYLKKLKDNGKVYNTGADAVQLFANGEVAMTVNGTWAAAAAKKAGKKLG 212

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1781386671 306 ---PNDTKFntnlidplvsegytqkrlnysetLGlWTSWGISANTKHLGRI-LQMVDWAYSEEAQNE 368
Cdd:pfam13416 213 avvPKDGSF-----------------------LG-GKGLVVPAGAKDPRLAaLDFIKFLTSPENQAA 255
PBP2_XBP1_like cd14749
The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; ...
 49-368 6.57e-06

The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold; This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270452 [Multi-domain]  Cd Length: 388  Bit Score: 48.53  E-value: 6.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  49 LLNNTSGDGAEFVFKELVKEkF-----NIDIKFSLNNNQSHFEKLNLLIASNELPDIVSPLPADRTKLIGPKGALVAVDE 123
Cdd:cd14749     4 YWQYFTGDTKKKYMDELIAD-FekenpNIKVKVVVFPYDNYKTKLKTAVAAGEGPDVFNLWPGGWLAEFVKAGLLLPLTD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 124 YFDylpnfvkylEEDETNKI-----SAMADDGHIYALPrFAVGKTDYKWTpiirQDYLEELNI-PVPTTYKELFDALRKI 197
Cdd:cd14749    83 YLD---------PNGVDKRFlpglaDAVTFNGKVYGIP-FAARALALFYN----KDLFEEAGGvKPPKTWDELIEAAKKD 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 198 KAAHPDTVGIVnrekmtfLKAFGVGYNTY-DTMFY-NKENDKFEFGPMNSGFK-EMITDFAQAWQDGVLDKEFFTASEQ- 273
Cdd:cd14749   149 KFKAKGQTGFG-------LLLGAQGGHWYfQYLVRqAGGGPLSDDGSGKATFNdPAFVQALQKLQDLVKAGAFQEGFEGi 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 274 ----QWQEkFLNGSGVFTLDWPKRAYTLKDSyqklNPNDtKFNTNLIdPLVSEGYtqkrlNYSETLGLWTSWGISANTKH 349
Cdd:cd14749   222 dyddAGQA-FAQGKAAMNIGGSWDLGAIKAG----EPGG-KIGVFPF-PTVGKGA-----QTSTIGGSDWAIAISANGKK 289

                         330
                  ....*....|....*....
gi 1781386671 350 LGRILQMVDWAYSEEAQNE 368
Cdd:cd14749   290 KEAAVKFLKYLTSPEVMKQ 308
DUF3502 pfam12010
Domain of unknown function (DUF3502); This presumed domain is functionally uncharacterized. ...
 372-398 3.10e-04

Domain of unknown function (DUF3502); This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 140 amino acids in length. This domain is found associated with pfam01547.


Pssm-ID: 463429  Cd Length: 131  Bit Score: 40.67  E-value: 3.10e-04
                          10        20
                  ....*....|....*....|....*..
gi 1781386671 372 GLEGKHYTVNEDGRYQYTPEMKASYNP 398
Cdd:pfam12010   1 GIEGVHYEKVGDGKIKLLPDGVDAYNP 27
PBP2_Maltodextrin cd13657
The periplasmic binding component of ABC transport system specific for maltodextrin; This ...
 71-237 4.21e-04

The periplasmic binding component of ABC transport system specific for maltodextrin; This group includes the periplasmic maltodextrin-binding protein of a binding protein-dependent ATP-binding cassette transporter. Maltodextrin is a polysaccharide that is used as a food addtive and can be enzymatically produced from any starch . Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270375 [Multi-domain]  Cd Length: 368  Bit Score: 42.75  E-value: 4.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671  71 NIDIKFSLNNNQShfEKLNLLIASNELPDIVSpLPADRTKLIGPKGALVAVDEYFDylpnfVKYLEEDETNKISAMADDG 150
Cdd:cd13657    31 NVKVPFEKKPDLQ--NKLLTAIPAGEGPDLFI-WAHDWIGQFAEAGLLVPISDYLS-----EDDFENYLPTAVEAVTYKG 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1781386671 151 HIYALPrFAvgktdYKWTPIIrqdYLEELNIPVPTTYKELFDALRKIKAAHPDTVGIV-NREKMTFLKAFGVGYNTYdtm 229
Cdd:cd13657   103 KVYGLP-EA-----YETVALI---YNKALVDQPPETTDELLAIMKDHTDPAAGSYGLAyQVSDAYFVSAWIFGFGGY--- 170


                  ....*...
gi 1781386671 230 FYNKENDK 237
Cdd:cd13657   171 YFDDETDK 178
 
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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