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Conserved domains on  [gi|500108775|ref|WP_011784780|]
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MULTISPECIES: phosphate/phosphite/phosphonate ABC transporter substrate-binding protein [Gammaproteobacteria]

Protein Classification

PBP2_PnhD_2 domain-containing protein( domain architecture ID 10194384)

PBP2_PnhD_2 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PBP2_PnhD_2 cd13572
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 26-274 1.32e-127

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


:

Pssm-ID: 270290 [Multi-domain]  Cd Length: 249  Bit Score: 362.79  E-value: 1.32e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  26 TDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPF 105
Cdd:cd13572    1 QAPETLKVGAIPDENPTTLIRLNDPLADYLEKELGVEVELVVVTDYAAMVEAMRNGQLDLAYFGGLTYVQARLKPGAEPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 106 AAMVVDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVA 185
Cdd:cd13572   81 AQLLRDGDPTFHSVFIANTDSGINSLADLKGKRFAFGDPASTSGHLMPRYFLLEAGVLPDGDFYRVGFSGAHDATALAVA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 186 NGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPEILDNLKAEGFAAI 265
Cdd:cd13572  161 NGKVDAGALNEAIWESLVEEGKIDGEKVKVIWRTPPYPDYPWTVRPNLGPELKEKVRNAFLSLDDPEVLDIFGASGFIPA 240


                 ....*....
gi 500108775 266 TDEDYDVIR 274
Cdd:cd13572  241 SDDDYDPIE 249
 
Name Accession Description Interval E-value
PBP2_PnhD_2 cd13572
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 26-274 1.32e-127

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270290 [Multi-domain]  Cd Length: 249  Bit Score: 362.79  E-value: 1.32e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  26 TDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPF 105
Cdd:cd13572    1 QAPETLKVGAIPDENPTTLIRLNDPLADYLEKELGVEVELVVVTDYAAMVEAMRNGQLDLAYFGGLTYVQARLKPGAEPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 106 AAMVVDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVA 185
Cdd:cd13572   81 AQLLRDGDPTFHSVFIANTDSGINSLADLKGKRFAFGDPASTSGHLMPRYFLLEAGVLPDGDFYRVGFSGAHDATALAVA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 186 NGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPEILDNLKAEGFAAI 265
Cdd:cd13572  161 NGKVDAGALNEAIWESLVEEGKIDGEKVKVIWRTPPYPDYPWTVRPNLGPELKEKVRNAFLSLDDPEVLDIFGASGFIPA 240


                 ....*....
gi 500108775 266 TDEDYDVIR 274
Cdd:cd13572  241 SDDDYDPIE 249
3A0109s03R TIGR01098
phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ...
 1-248 8.35e-98

phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions]


Pssm-ID: 273442 [Multi-domain]  Cd Length: 254  Bit Score: 287.71  E-value: 8.35e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775    1 MKTMIHSLLALIMMLGI---HWSAHAADTDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEA 77
Cdd:TIGR01098   1 MKRLLALLAALLGASLAaacSKKAAEAAAVPKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   78 MRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVV--DGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKT 155
Cdd:TIGR01098  81 MRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVstDGSPGYYSVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  156 VLLEKAELEA-GKDYEAHFVGSHDAVAVNVANGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLA 234
Cdd:TIGR01098 161 QLKKEGGLDAdGFFSEVVFSGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLP 240

                         250
                  ....*....|....
gi 500108775  235 PELKSNIQKAFLQI 248
Cdd:TIGR01098 241 PELKEKIRDAFLTL 254
Phosphonate-bd pfam12974
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
 33-270 7.29e-91

ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.


Pssm-ID: 432911 [Multi-domain]  Cd Length: 243  Bit Score: 269.52  E-value: 7.29e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   33 VALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMV-VD 111
Cdd:pfam12974   1 FGVLPDESPDELKARYQPLADYLSEELGVPVELVVATDYAAVVEALRAGQVDIAYFGPLAYVQAVDRAGAEPLATPVePD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  112 GKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVANGNADA 191
Cdd:pfam12974  81 GSAGYRSVIIVRKDSPIQSLEDLKGKTVAFGDPSSTSGYLVPLALLFAEAGLDPEDDFKPVFSGSHDAVALAVLNGDADA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  192 GGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQID----DPEILDNLKAEGFAAITD 267
Cdd:pfam12974 161 GAVNSEVLERLVAEGPIDRDQLRVIAESPPIPNDPLVARPDLPPELKEKIRDALLALDetpeGRKVLEALGIDGFVPADD 240


                  ...
gi 500108775  268 EDY 270
Cdd:pfam12974 241 SDY 243
PhnD COG3221
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ...
 35-276 6.15e-90

ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 442454 [Multi-domain]  Cd Length: 250  Bit Score: 267.56  E-value: 6.15e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  35 LLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVVDGKP 114
Cdd:COG3221    1 VLPSESPADLLARWQPLADYLEEELGVPVELVPATDYAALIEALRAGQVDLAFLGPLPYVLARDRAGAEPLATPVRDGSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 115 TYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTvLLEKAELEAGKDY-EAHFVGSHDAVAVNVANGNADAGG 193
Cdd:COG3221   81 GYRSVIIVRADSPIKSLEDLKGKRFAFGDPDSTSGYLVPRA-LLAEAGLDPERDFsEVVFSGSHDAVILAVANGQADAGA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 194 LSEVIFEHVMDRGLiDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQID----DPEILDNLKAEGFAAITDED 269
Cdd:COG3221  160 VDSGVLERLVEEGP-DADQLRVIWESPPIPNDPFVARPDLPPELREKIREALLSLDedpeGKAILEALGLEGFVPADDAD 238


                 ....*..
gi 500108775 270 YDVIRAM 276
Cdd:COG3221  239 YDPIREL 245
PRK11553 PRK11553
alkanesulfonate transporter substrate-binding subunit; Provisional
 9-191 7.99e-08

alkanesulfonate transporter substrate-binding subunit; Provisional


Pssm-ID: 236929  Cd Length: 314  Bit Score: 52.48  E-value: 7.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   9 LALIMMLGIHWSAHAADTDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTtdySSMIEAMRFGRIDLAyf 88
Cdd:PRK11553   7 LALAGLLSVSTLAVAAESSPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAG---PQMLEALNVGSIDLG-- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  89 gplsyvmakSKSDIEPFAAM----------VVDGKPTYRSIIIANaDSGVGSFADIKGKKMAYgDRASTSSHLIPKtvLL 158
Cdd:PRK11553  82 ---------STGDIPPIFAQaagadlvyvgVEPPKPKAEVILVAE-NSPIKTVADLKGHKVAF-QKGSSSHNLLLR--AL 148

                        170       180       190
                 ....*....|....*....|....*....|...
gi 500108775 159 EKAELEAgKDYEAHFVGSHDAVAVnVANGNADA 191
Cdd:PRK11553 149 RKAGLKF-TDIQPTYLTPADARAA-FQQGNVDA 179
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 59-248 8.73e-08

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 51.56  E-value: 8.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775    59 LGKEVElIVTTDYSSMIEAMRFGRIDLAyFGPLSYVMAKSKSdiepfaamVVDGKPTYRS--IIIANADSGVGSFADIKG 136
Cdd:smart00062  37 LGLKVE-FVEVSFDSLLTALKSGKIDVV-AAGMTITPERAKQ--------VDFSDPYYRSgqVILVRKDSPIKSLEDLKG 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   137 KKMAygdrastsshlIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVANGNADAGGLSE-VIFEHVMDRGLIDrskVKV 215
Cdd:smart00062 107 KKVA-----------VVAGTTAEELLKKLYPEAKIVSYDSNAEALAALKAGRADAAVADApLLAALVKQHGLPE---LKI 172

                          170       180       190
                   ....*....|....*....|....*....|....
gi 500108775   216 LGYSGDFP-QYPWAMRSNlAPELKSNIQKAFLQI 248
Cdd:smart00062 173 VPDPLDTPeGYAIAVRKG-DPELLDKINKALKEL 205
 
Name Accession Description Interval E-value
PBP2_PnhD_2 cd13572
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 26-274 1.32e-127

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270290 [Multi-domain]  Cd Length: 249  Bit Score: 362.79  E-value: 1.32e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  26 TDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPF 105
Cdd:cd13572    1 QAPETLKVGAIPDENPTTLIRLNDPLADYLEKELGVEVELVVVTDYAAMVEAMRNGQLDLAYFGGLTYVQARLKPGAEPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 106 AAMVVDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVA 185
Cdd:cd13572   81 AQLLRDGDPTFHSVFIANTDSGINSLADLKGKRFAFGDPASTSGHLMPRYFLLEAGVLPDGDFYRVGFSGAHDATALAVA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 186 NGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPEILDNLKAEGFAAI 265
Cdd:cd13572  161 NGKVDAGALNEAIWESLVEEGKIDGEKVKVIWRTPPYPDYPWTVRPNLGPELKEKVRNAFLSLDDPEVLDIFGASGFIPA 240


                 ....*....
gi 500108775 266 TDEDYDVIR 274
Cdd:cd13572  241 SDDDYDPIE 249
3A0109s03R TIGR01098
phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are ...
 1-248 8.35e-98

phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein; Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions]


Pssm-ID: 273442 [Multi-domain]  Cd Length: 254  Bit Score: 287.71  E-value: 8.35e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775    1 MKTMIHSLLALIMMLGI---HWSAHAADTDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEA 77
Cdd:TIGR01098   1 MKRLLALLAALLGASLAaacSKKAAEAAAVPKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   78 MRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVV--DGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKT 155
Cdd:TIGR01098  81 MRFGRVDIAWFGPSSYVLAHYRANAEVFALTAVstDGSPGYYSVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRY 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  156 VLLEKAELEA-GKDYEAHFVGSHDAVAVNVANGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLA 234
Cdd:TIGR01098 161 QLKKEGGLDAdGFFSEVVFSGSHDASALAVANGKVDAATNNSSAIGRLKKRGPSDMKKVRVIWKSPLIPNDPIAVRKDLP 240

                         250
                  ....*....|....
gi 500108775  235 PELKSNIQKAFLQI 248
Cdd:TIGR01098 241 PELKEKIRDAFLTL 254
Phosphonate-bd pfam12974
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
 33-270 7.29e-91

ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake.


Pssm-ID: 432911 [Multi-domain]  Cd Length: 243  Bit Score: 269.52  E-value: 7.29e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   33 VALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMV-VD 111
Cdd:pfam12974   1 FGVLPDESPDELKARYQPLADYLSEELGVPVELVVATDYAAVVEALRAGQVDIAYFGPLAYVQAVDRAGAEPLATPVePD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  112 GKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVANGNADA 191
Cdd:pfam12974  81 GSAGYRSVIIVRKDSPIQSLEDLKGKTVAFGDPSSTSGYLVPLALLFAEAGLDPEDDFKPVFSGSHDAVALAVLNGDADA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  192 GGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQID----DPEILDNLKAEGFAAITD 267
Cdd:pfam12974 161 GAVNSEVLERLVAEGPIDRDQLRVIAESPPIPNDPLVARPDLPPELKEKIRDALLALDetpeGRKVLEALGIDGFVPADD 240


                  ...
gi 500108775  268 EDY 270
Cdd:pfam12974 241 SDY 243
PBP2_PhnD_like cd01071
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
 26-274 5.58e-90

Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily; This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270232 [Multi-domain]  Cd Length: 253  Bit Score: 267.59  E-value: 5.58e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  26 TDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPF 105
Cdd:cd01071    1 AAPKELRFGLVPAEDADELKKEFEPLADYLEEELGVPVELVVATSYAAVVEAMRNGKVDIAWLGPASYVLAHDRAGAEAL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 106 AAMVVDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVA 185
Cdd:cd01071   81 ATEVRDGSPGYYSVIIVRKDSPIKSLEDLKGKTVAFVDPSSTSGYLFPRAMLKDAGIDPPDFFFEVVFAGSHDSALLAVA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 186 NGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPE----ILDNLKAEG 261
Cdd:cd01071  161 NGDVDAAATYDSTLERAAAAGPIDPDDLRVIWRSPPIPNDPLVVRKDLPPALKAKIRDALLDLDETDegqkLLAGLGLTG 240

                        250
                 ....*....|...
gi 500108775 262 FAAITDEDYDVIR 274
Cdd:cd01071  241 FVPATDDDYDPIR 253
PhnD COG3221
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ...
 35-276 6.15e-90

ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 442454 [Multi-domain]  Cd Length: 250  Bit Score: 267.56  E-value: 6.15e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  35 LLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVVDGKP 114
Cdd:COG3221    1 VLPSESPADLLARWQPLADYLEEELGVPVELVPATDYAALIEALRAGQVDLAFLGPLPYVLARDRAGAEPLATPVRDGSP 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 115 TYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTvLLEKAELEAGKDY-EAHFVGSHDAVAVNVANGNADAGG 193
Cdd:COG3221   81 GYRSVIIVRADSPIKSLEDLKGKRFAFGDPDSTSGYLVPRA-LLAEAGLDPERDFsEVVFSGSHDAVILAVANGQADAGA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 194 LSEVIFEHVMDRGLiDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQID----DPEILDNLKAEGFAAITDED 269
Cdd:COG3221  160 VDSGVLERLVEEGP-DADQLRVIWESPPIPNDPFVARPDLPPELREKIREALLSLDedpeGKAILEALGLEGFVPADDAD 238


                 ....*..
gi 500108775 270 YDVIRAM 276
Cdd:COG3221  239 YDPIREL 245
PhnD TIGR03431
phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset ...
 2-276 1.16e-65

phosphonate ABC transporter, periplasmic phosphonate binding protein; This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.


Pssm-ID: 132472 [Multi-domain]  Cd Length: 288  Bit Score: 206.82  E-value: 1.16e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775    2 KTMIHSLLALIMMLGIHwsAHAADTdPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFG 81
Cdd:TIGR03431   3 RRLILSLVAAFMLISSN--AQAEDW-PKELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   82 RIDLAYFGPLSYVMAKSKSDIEPFAAMV-VDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEK 160
Cdd:TIGR03431  80 KVDIAWYGPSSYAEAYQKANAEAFAIEVnADGSTGYYSVLIVKKDSPIKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  161 AELEAgKDY--EAHFVGSHDAVAVNVANGNADAGGLSEVIFEHVMDRGLID-RSKVKVLGYSGDFPQYPWAMRSNLAPEL 237
Cdd:TIGR03431 160 NGIKP-KEYfkKVTFSGSHEAAILAVANGTVDAATTNDENLDRMIRKGQPDaMEDLRIIWKSPLIPNGPIVYRKDLPADL 238

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 500108775  238 KSNIQKAFLQIDD-----PEILDNLKAEGFAAITDEDYDVIRAM 276
Cdd:TIGR03431 239 KAKIRKAFLNYHKtdkacFEKIAGGDLKGFVAASDKDYDPIRDL 282
PBP2_PnhD_4 cd13574
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 31-274 4.87e-65

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270292 [Multi-domain]  Cd Length: 250  Bit Score: 204.08  E-value: 4.87e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  31 LKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAK-SKSDIEPFAAMV 109
Cdd:cd13574    6 LRFGVHPYLSPTELVKRFQPLLDYLEEELGRPVEIKVSKDYQEHVDRLGSGKIDIAYLGPAPYVQAKdRRYGIKPLLALL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 110 -VDGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKA-ELEAGKDYEahFVGSHDAVAVNVANG 187
Cdd:cd13574   86 eTDGKPTYNGVIVVRADSPIKSLADLAGKSFAFGDPLSTMGHLVPRAMLRQAGiTSLDLAGYD--YLGRHDNVALAVLAG 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 188 NADAGGLSEVIFEHVMDRGLidrskvKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDP------EILDNLKAEG 261
Cdd:cd13574  164 EFDAGALKEEVYRKYKGRGL------RVLATSPPLPGHALVARATLPEELVKALRRALLELDSTgaglaiLTWIEELRHG 237

                        250
                 ....*....|...
gi 500108775 262 FAAITDEDYDVIR 274
Cdd:cd13574  238 FVPVTDEDYDLLR 250
PBP2_PnhD_1 cd13571
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 31-274 1.95e-64

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding components of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270289 [Multi-domain]  Cd Length: 253  Bit Score: 202.49  E-value: 1.95e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  31 LKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVV 110
Cdd:cd13571    6 LRIGLASVLSPRETLALYDPLAEYLERKLGRPVEFVQRRTYAEINELLKNGKVDLAFVCSGAYVQARDKAGLELLAVPEI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 111 DGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPkTVLLEKAELEAGKDY-EAHFVGSHDAVAVNVANGNA 189
Cdd:cd13571   86 NGQPTYRSYIIVPADSPAKSLEDLKGKRFAFTDPLSNSGFLVP-MYLLAELGLDPERFFsRVFFTGSHDKSIQAVANGLV 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 190 DAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQI-DDPE---ILDNLKAEGFAAI 265
Cdd:cd13571  165 DGAAVDSLVYEYAVEKGPELAANVRIIWRSEPIGNPPVVARPGLDPELKAALQEAFLSMhEDPEgraALEGLGIDRFVPA 244


                 ....*....
gi 500108775 266 TDEDYDVIR 274
Cdd:cd13571  245 DDSLYDPIR 253
ABC_peri_selen TIGR04553
putative selenate ABC transporter periplasmic binding protein; Members of this family ABC ...
 31-281 2.24e-52

putative selenate ABC transporter periplasmic binding protein; Members of this family ABC transporter periplasmic binding proteins and represent one clade within a larger family that includes phosphate, phosphite, and phosphonate transporters. All members of the seed alignment occur near a gene for SelD, the selenium-activating protein needed to make selenocysteine or selenouridine. Context therefore suggests members should be able to transport selenate, although transporting other substrates as well (e.g. phosphonates) is possible. This model has no overlap with TIGR03431, whose members are found regularly with phosphonate catabolism operons.


Pssm-ID: 275346 [Multi-domain]  Cd Length: 266  Bit Score: 172.26  E-value: 2.24e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   31 LKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKS-DIEPFAAMV 109
Cdd:TIGR04553   2 FVFTAIPDEDPTELQRRFAPLADYLEEELGVEVRFVPVTDYAAAVEAFRNNQVQLAWFGGLTGVQARVRVpGSVPLAQRV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  110 VDGKptYRSIIIANADSG---VGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAElEAGKDYE-AHFVGSHDAVAVNVA 185
Cdd:TIGR04553  82 EDEA--FRSVFIAHESTIlelADGLPELKGKTFTFGSKSSTSGRLMPRSFLLEAGE-APDDDFKrVGYSGAHDATLALVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  186 NGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPE----LKSNIQKAFLQID-----DPEILDN 256
Cdd:TIGR04553 159 AGTYDAGALNISVWEKEVADGKVDTDKVRVIWTTPGYPDYNWTVRGDVDERfgegFTDKVTQALLDLDpstaeDKEILEL 238

                         250       260
                  ....*....|....*....|....*...
gi 500108775  257 LKAEGFAAITDEDYDVIRAMG---GLLN 281
Cdd:TIGR04553 239 FRASRFIPTSNDNYAGIEAAAreaGLLD 266
PBP2_PnhD_3 cd13573
Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains ...
 27-273 1.93e-43

Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold; This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270291 [Multi-domain]  Cd Length: 253  Bit Score: 148.78  E-value: 1.93e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  27 DPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYF--GPLSYvmAKSKSDIEP 104
Cdd:cd13573    2 DPDTLVFAYTPVEDPAVYQEIWAPFIAHISKVTGKDVQFYPVQSNAAQTEAMRSGRLHIAGFstGPTPF--AVNLAGAVP 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 105 FAAMVV-DGKPTYRSIIIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVN 183
Cdd:cd13573   80 FAVKGYeDGSFGYELEVITRIDSGIQKVKDLKGRKVAHTSPTSNSGHLAPRALFPAQGGIVPDKDYEVTFSGKHDQSILG 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 184 VANGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPeilDNLKAEG-- 261
Cdd:cd13573  160 VFNGDYDAAPVASDVLERMAERGQVKEEQFRVIYKSFAFPTGPFGYAHNLKPELREKIKEAFFTYDFA---GTKLAEIfa 236

                        250
                 ....*....|....*..
gi 500108775 262 ----FAAIT-DEDYDVI 273
Cdd:cd13573  237 gfdrFAPITyKEHWAVI 253
PBP2_PnhD cd13575
Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 ...
 27-274 6.15e-30

Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 periplasmic binding fold; This subfamily includes the Escherichia coli PhnD (EcPhnD) which exhibits high affinity for the environmentally abundant 2-aminoethylphosphonate (2-AEP), a precursor in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans. The Escherichia coli phn operon encodes 14 genes involved in binding, uptake and metabolism of phosphonate, and is activated under phophophate-limiting conditions. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate.


Pssm-ID: 270293 [Multi-domain]  Cd Length: 259  Bit Score: 113.33  E-value: 6.15e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  27 DPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFA 106
Cdd:cd13575    2 DEKALNFGIISTESQQNLRAQWEPFLAAMEKKLGVKVNAFFAPDYAGIIEGMRFNKVQIAWYGNKSAMEAVDRANGEVFA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 107 AMV-VDGKPTYRSIIIANADSGVGSFADI--KGKKM--AYGDRASTSSHLIPKTVLLEKAELEAGKDYEAHFVGSHDAVA 181
Cdd:cd13575   82 QTVaADGSPGYYSHLIVNKDSPINSLNDVlaKAKDLtfGNGDPNSTSGFLVPGYYVFAKNGIDPKKFFKRTVNANHETNA 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 182 VNVANGNADAGGLSEVIFEHVMDRGLIDRSKVKVLGYSGDFPQYPWAMRSNLAPELKSNIQKAFLQIDDPEI-----LDN 256
Cdd:cd13575  162 LAVANKQVDVATNNTENLDRLKERAPEKLKQLRIIWTSPLIPGDPLVWRKDLPEAVKKKIADFFFGYGQTAEeksvlKER 241

                        250
                 ....*....|....*...
gi 500108775 257 LKAEGFAAITDEDYDVIR 274
Cdd:cd13575  242 LDWSPFKPSSDGQLVPIR 259
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 7-226 1.54e-12

ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 66.57  E-value: 1.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   7 SLLALIMMLGIHWSAHAADTDPdlLKVALLPDENASELI--KRNQPLKDYlettlGKEVELIVTTDYSSMIEAMRFGRID 84
Cdd:COG0715    2 AALAALALAACSAAAAAAEKVT--LRLGWLPNTDHAPLYvaKEKGYFKKE-----GLDVELVEFAGGAAALEALAAGQAD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  85 LAYFGPLSYVMAKSK-SDIEPFAAMVVDGkptyRSIIIANADSGVGSFADIKGKKMAYGdRASTSSHLIPKtvLLEKAEL 163
Cdd:COG0715   75 FGVAGAPPALAARAKgAPVKAVAALSQSG----GNALVVRKDSGIKSLADLKGKKVAVP-GGSTSHYLLRA--LLAKAGL 147

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500108775 164 EAgKDYEAHFVGSHDAVAvNVANGNADAGglseVIFEHVMDRgLIDRSKVKVLGYSGD-FPQYP 226
Cdd:COG0715  148 DP-KDVEIVNLPPPDAVA-ALLAGQVDAA----VVWEPFESQ-AEKKGGGRVLADSADlVPGYP 204
PBP2_NrtA_SsuA_CpmA_like cd01008
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ...
 56-236 4.69e-12

Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270229 [Multi-domain]  Cd Length: 212  Bit Score: 63.85  E-value: 4.69e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  56 ETTLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSK-SDIEPFAAMVVDGKPTYrsiIIANADSGVGSFADI 134
Cdd:cd01008   26 KEKEGIDVEWVEFTSGPPALEALAAGSLDFGTGGDTPALLAAAGgVPVVLIAALSRSPNGNG---IVVRKDSGITSLADL 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 135 KGKKMAYGdrASTSSHLIPKTVlLEKAELEAgKDYEAHFVGSHDAVAvNVANGNADAGglseVIFEHVMDRgLIDRSKVK 214
Cdd:cd01008  103 KGKKIAVT--KGTTGHFLLLKA-LAKAGLSV-DDVELVNLGPADAAA-ALASGDVDAW----VTWEPFLSL-AEKGGDAR 172

                        170       180
                 ....*....|....*....|....*
gi 500108775 215 VLGYSGDFPQYP---WAMRSNLAPE 236
Cdd:cd01008  173 IIVDGGGLPYTDpsvLVARRDFVEE 197
PBP2_NrtA_CpmA_like cd13553
Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ...
 60-222 1.72e-09

Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding their ligand with high affinity, they 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. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270271 [Multi-domain]  Cd Length: 212  Bit Score: 56.43  E-value: 1.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  60 GKEVELIVTTDYSSMIEAMRFGRIDLAYFG-PLSYVMAKSK-SDIEPFAAMVVDGkptyrSIIIANADSGVGSFADIKGK 137
Cdd:cd13553   28 GLDVELVKFPSWADLRDALAAGELDAAHVLaPMPAAATYGKgAPIKVVAGLHRNG-----SAIVVSKDSGIKSVADLKGK 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 138 KMAYGDRASTsSHLIPKTvLLEKAELEAGKDYEAHFVGSHDAVAvNVANGNADAGGLSE----------VIFEHVMDRGL 207
Cdd:cd13553  103 TIAVPFPGST-HDVLLRY-WLAAAGLDPGKDVEIVVLPPPDMVA-ALAAGQIDAYCVGEpwnaravaegVGRVLADSGDI 179

                        170
                 ....*....|....*
gi 500108775 208 IDRSKVKVLGYSGDF 222
Cdd:cd13553  180 WPGHPCCVLVVREDF 194
PBP2_SsuA_like_2 cd13558
Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding ...
 74-191 1.32e-08

Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270276  Cd Length: 267  Bit Score: 54.60  E-value: 1.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  74 MIEAMRFGRIDLAYFGPLSYV-MAKSKSDIEPFAAMVVDGKPTYrsiIIANADSGVGSFADIKGKKMAYGdRASTSSHLI 152
Cdd:cd13558   39 LLEALRAGALDIGGAGDTPPLfAAAAGAPIKIVAALRGDVNGQA---LLVPKDSPIRSVADLKGKRVAYV-RGSISHYLL 114

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 500108775 153 PKTvlLEKAELeAGKDYEAHFVGSHDAVAVnVANGNADA 191
Cdd:cd13558  115 LKA--LEKAGL-SPSDVELVFLTPADALAA-FASGQVDA 149
PRK11553 PRK11553
alkanesulfonate transporter substrate-binding subunit; Provisional
 9-191 7.99e-08

alkanesulfonate transporter substrate-binding subunit; Provisional


Pssm-ID: 236929  Cd Length: 314  Bit Score: 52.48  E-value: 7.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   9 LALIMMLGIHWSAHAADTDPDLLKVALLPDENASELIKRNQPLKDYLETTLGKEVELIVTtdySSMIEAMRFGRIDLAyf 88
Cdd:PRK11553   7 LALAGLLSVSTLAVAAESSPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAG---PQMLEALNVGSIDLG-- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  89 gplsyvmakSKSDIEPFAAM----------VVDGKPTYRSIIIANaDSGVGSFADIKGKKMAYgDRASTSSHLIPKtvLL 158
Cdd:PRK11553  82 ---------STGDIPPIFAQaagadlvyvgVEPPKPKAEVILVAE-NSPIKTVADLKGHKVAF-QKGSSSHNLLLR--AL 148

                        170       180       190
                 ....*....|....*....|....*....|...
gi 500108775 159 EKAELEAgKDYEAHFVGSHDAVAVnVANGNADA 191
Cdd:PRK11553 149 RKAGLKF-TDIQPTYLTPADARAA-FQQGNVDA 179
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 59-248 8.73e-08

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 51.56  E-value: 8.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775    59 LGKEVElIVTTDYSSMIEAMRFGRIDLAyFGPLSYVMAKSKSdiepfaamVVDGKPTYRS--IIIANADSGVGSFADIKG 136
Cdd:smart00062  37 LGLKVE-FVEVSFDSLLTALKSGKIDVV-AAGMTITPERAKQ--------VDFSDPYYRSgqVILVRKDSPIKSLEDLKG 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   137 KKMAygdrastsshlIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVANGNADAGGLSE-VIFEHVMDRGLIDrskVKV 215
Cdd:smart00062 107 KKVA-----------VVAGTTAEELLKKLYPEAKIVSYDSNAEALAALKAGRADAAVADApLLAALVKQHGLPE---LKI 172

                          170       180       190
                   ....*....|....*....|....*....|....
gi 500108775   216 LGYSGDFP-QYPWAMRSNlAPELKSNIQKAFLQI 248
Cdd:smart00062 173 VPDPLDTPeGYAIAVRKG-DPELLDKINKALKEL 205
PBP2_SsuA cd13557
Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic ...
 43-191 1.27e-06

Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes the sulfonate binding domains SsuA found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270275  Cd Length: 275  Bit Score: 48.83  E-value: 1.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  43 ELIKRNQPLKDYLETtLGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSK-SDIEPFAamVVDGKPTYRSIII 121
Cdd:cd13557   13 VLLKARGELEKRLKP-LGVKVTWSEFPAGPQLLEALNVGSIDFGSTGDTPPIFAQAAgAPLVYVA--VEPPTPKGEAILV 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 122 ANaDSGVGSFADIKGKKMAYGdRASTSSHLIPKtvLLEKAELEAgKDYEAHFVGSHDAVAVnVANGNADA 191
Cdd:cd13557   90 PK-DSPIKTVADLKGKKIAFQ-KGSSAHYLLVK--ALEKAGLTL-DDIEPVYLSPADARAA-FEQGQVDA 153
PBP2_SsuA_like_6 cd13563
Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 ...
 60-223 3.05e-06

Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270281 [Multi-domain]  Cd Length: 208  Bit Score: 46.84  E-value: 3.05e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  60 GKEVELIVTTDYSSMIEAMRFGRIDLAYFGpLSYVMAKSKSDIEPFAAMVVDGKPTYRSIIianADSGVGSFADIKGKKM 139
Cdd:cd13563   28 GLDVELVWFESYSDSMAALASGQIDAAATT-LDDALAMAAKGVPVKIVLVLDNSNGADGIV---AKPGIKSIADLKGKTV 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 140 AYgdRASTSSHLIPKTVlLEKAELeAGKDYEAHFVGSHDAVAVNVAnGNADAGglseVIFEHVMDRGLiDRSKVKVLGYS 219
Cdd:cd13563  104 AV--EEGSVSHFLLLNA-LEKAGL-TEKDVKIVNMTAGDAGAAFIA-GQVDAA----VTWEPWLSNAL-KRGKGKVLVSS 173


                 ....
gi 500108775 220 GDFP 223
Cdd:cd13563  174 ADTP 177
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 59-264 3.79e-06

ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms];


Pssm-ID: 440596 [Multi-domain]  Cd Length: 223  Bit Score: 46.90  E-value: 3.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  59 LGKEVElIVTTDYSSMIEAMRFGRIDLAyFGPLSYVMAKSKsdiepfaamVVD-GKPTYRS---IIIANADSGVGSFADI 134
Cdd:COG0834   36 LGLKVE-FVPVPWDRLIPALQSGKVDLI-IAGMTITPEREK---------QVDfSDPYYTSgqvLLVRKDNSGIKSLADL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 135 KGKKMAYGdRASTSSHLIPKtvLLEKAELEAGKDYEahfvgshDAVAvNVANGNADAGGLSEVIFEHVMDRGliDRSKVK 214
Cdd:COG0834  105 KGKTVGVQ-AGTTYEEYLKK--LGPNAEIVEFDSYA-------EALQ-ALASGRVDAVVTDEPVAAYLLAKN--PGDDLK 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 500108775 215 VLGYSGDFPQYPWAMRSNlAPELKSNIQKAflqiddpeiLDNLKAEGFAA 264
Cdd:COG0834  172 IVGEPLSGEPYGIAVRKG-DPELLEAVNKA---------LAALKADGTLD 211
Imp COG2358
TRAP-type uncharacterized transport system, periplasmic component [General function prediction ...
 120-195 3.80e-06

TRAP-type uncharacterized transport system, periplasmic component [General function prediction only];


Pssm-ID: 441925 [Multi-domain]  Cd Length: 303  Bit Score: 47.53  E-value: 3.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500108775 120 IIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKtvLLEKAELEAgKDYEAHFVGSHDAVAvNVANGNADAGGLS 195
Cdd:COG2358  106 LVVRADSGIKSLADLKGKRVSVGPPGSGTEVTAER--LLEAAGLTY-DDVKVEYLGYGEAAD-ALKDGQIDAAFFV 177
PBP2_TAXI_TRAP cd13520
Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic ...
 120-191 1.99e-05

Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold; This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. The substrate-binding domain of TAXI proteins belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises 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. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and tworeceptor cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270238 [Multi-domain]  Cd Length: 285  Bit Score: 45.30  E-value: 1.99e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 500108775 120 IIANADSGVGSFADIKGKKMAYGDRASTSSHLIPKtvLLEKAELEaGKDYEAHFVGSHDAVAvNVANGNADA 191
Cdd:cd13520   94 LVVRKDSGIKSIADLKGKRVAVGPPGSGTELTARR--LLEAYGLT-DDDVKAEYLGLSDAAD-ALKDGQIDA 161
PBP2_peptides_like cd13530
Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This ...
 59-262 6.33e-05

Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold; This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, 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 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. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 270248 [Multi-domain]  Cd Length: 217  Bit Score: 43.01  E-value: 6.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  59 LGKEVElIVTTDYSSMIEAMRFGRIDLAYFGplsyvMAksksdIEPFAAMVVD-GKPTYRS--IIIANADSGVGS-FADI 134
Cdd:cd13530   37 LGVKVE-FVDTDFDGLIPALQSGKIDVAISG-----MT-----ITPERAKVVDfSDPYYYTgqVLVVKKDSKITKtVADL 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775 135 KGKKMAYGdRASTSshlipktvllEKAELEAGKDYEAHFVGSHDAVAVNVANGNADAGGLSEVIFEHVMDRGlidRSKVK 214
Cdd:cd13530  106 KGKKVGVQ-AGTTG----------EDYAKKNLPNAEVVTYDNYPEALQALKAGRIDAVITDAPVAKYYVKKN---GPDLK 171

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 500108775 215 VLGYSGDFPQYPWAMRSNlAPELKSNIQKAflqiddpeiLDNLKAEGF 262
Cdd:cd13530  172 VVGEPLTPEPYGIAVRKG-NPELLDAINKA---------LAELKADGT 209
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
 52-196 9.12e-05

ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other]


Pssm-ID: 130789 [Multi-domain]  Cd Length: 288  Bit Score: 43.12  E-value: 9.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   52 KDYLETTLGKE-VELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSDIEPFAAMVVDGKPTyrsIIIANADSGVGS 130
Cdd:TIGR01728  19 KGLLEKELGKTkVEWVEFPAGPPALEALGAGSLDFGYIGPGPALFAYAAGADIKAVGLVSDNKAT---AIVVIKGSPIRT 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500108775  131 FADIKGKKMAYgdRASTSSHLipktvLLEKAELEAG---KDYEAHFVGSHDAVAVnVANGNADAGGLSE 196
Cdd:TIGR01728  96 VADLKGKRIAV--PKGGSGHD-----LLLRALLKAGlsgDDVTILYLGPSDARAA-FAAGQVDAWAIWE 156
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
 49-192 9.16e-05

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.


Pssm-ID: 270214 [Multi-domain]  Cd Length: 196  Bit Score: 42.56  E-value: 9.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  49 QPLKDYLETTLGKEVELIVTTDYSSMIEAMRFGRIDLAyFGPLSYVMAKSKsDIEPFAAMV-VDGKPTYRSIIIANADS- 126
Cdd:cd00648   17 EDAAKQLAKETGIKVELVPGSSIGTLIEALAAGDADVA-VGPIAPALEAAA-DKLAPGGLYiVPELYVGGYVLVVRKGSs 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500108775 127 --GVGSFADIKGKKMAYGDRASTSSHLIpkTVLLEKAELEaGKDYEAHFVGSHDAVAVNVANGNADAG 192
Cdd:cd00648   95 ikGLLAVADLDGKRVGVGDPGSTAVRQA--RLALGAYGLK-KKDPEVVPVPGTSGALAAVANGAVDAA 159
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in ...
 59-248 1.03e-04

Bacterial extracellular solute-binding proteins, family 3; This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 425719 [Multi-domain]  Cd Length: 221  Bit Score: 42.66  E-value: 1.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   59 LGKEVElIVTTDYSSMIEAMRFGRIDLAyFGPLSY------VMAKSKSDIEPFAAMVVDGKptyrsiiiaNADSGVGSFA 132
Cdd:pfam00497  36 LGVKVE-FVPVSWDGLIPALQSGKVDLI-IAGMTItperakQVDFSDPYYYSGQVILVRKK---------DSSKSIKSLA 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  133 DIKGKKMAygdrastsshLIPKTVLLEKAELEAGKDYEAHFVGSHDAVAVNVANGNADAGGLSEVIFEHVMDRGliDRSK 212
Cdd:pfam00497 105 DLKGKTVG----------VQKGSTAEELLKNLKLPGAEIVEYDDDAEALQALANGRVDAVVADSPVAAYLIKKN--PGLN 172

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 500108775  213 VKVLGYSGDFPQYPWAMRSNlAPELKSNIQKAFLQI 248
Cdd:pfam00497 173 LVVVGEPLSPEPYGIAVRKG-DPELLAAVNKALAEL 207
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
 60-192 4.05e-04

NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine.3]. They are regulated by thiamine. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor.


Pssm-ID: 430398 [Multi-domain]  Cd Length: 216  Bit Score: 40.67  E-value: 4.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   60 GKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKS-DIEPFAAmVVDgKPTyrSIIIANADSGVGSFADIKGKK 138
Cdd:pfam09084  20 GLDVEIVEPADPSDATQLVASGKADFGVSYQESVLLARAKGlPVVSVAA-LIQ-HPL--SGVISLKDSGIKSPKDLKGKR 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 500108775  139 MAYGDrASTSSHLIpkTVLLEKAELEAgKDYEAHFVGShDAVAVNVANGNADAG 192
Cdd:pfam09084  96 IGYSG-SPFEEALL--KALLKKDGGDP-DDVTIVNVGG-MNLFPALLTGKVDAA 144
PBP2_sulfate_ester_like cd13555
Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This ...
 76-231 5.23e-04

Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270273  Cd Length: 268  Bit Score: 40.78  E-value: 5.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  76 EAMRFGRIDLAYFGPLSYVMAKSKS-DIEpfaaMVVDGKPTYRSIIIANADSGVGSFADIKGKKMAYGdrASTSSHLIPK 154
Cdd:cd13555   55 EAFANGQIDFAVYGDLPAIIGRAAGlDTK----LLLSSGSGNNAYLVVPPDSTIKSVKDLKGKKVAVQ--KGTAWQLTFL 128

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500108775 155 TVLLEKAELEagKDYEAHFVGSHDAVAVnVANGNADAG-GLSEVIFehVMDRGLIdrskvKVLGYSGDFPQyPWAMRS 231
Cdd:cd13555  129 RILAKNGLSE--KDFKIVNLDAQDAQAA-LASGDVDAAfTGYEALK--LEDQGAG-----KIIWSTKDKPE-DWTTQS 195
PBP2_SsuA_like_4 cd13561
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ...
 59-194 1.16e-03

Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold; This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts 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. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270279 [Multi-domain]  Cd Length: 212  Bit Score: 39.28  E-value: 1.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  59 LGKEVELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSdIEPFAAMVVDGKPTYrsiIIANADSGVGSFADIKGKK 138
Cdd:cd13561   28 HGLDPDFIEFTSGPPLVAALGSGSLDVGYTGPVAFNLPASGQ-AKVVLINNLENATAS---LIVRADSGIASIADLKGKK 103

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 500108775 139 MayGDRASTSSHLIPKtVLLEKAELeAGKDYEahFVGSHDAVAVN-VANGNADAGGL 194
Cdd:cd13561  104 I--GTPSGTTADVALD-LALRKAGL-SEKDVQ--IVNMDPAEIVTaFTSGSVDAAAL 154
NMT1_3 pfam16868
NMT1-like family;
75-147 1.96e-03

NMT1-like family;


Pssm-ID: 435616 [Multi-domain]  Cd Length: 289  Bit Score: 39.16  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775   75 IEAMRFGRIDLAYFGPLSYVMAKSKSdiEPFAAMvvDGKPTYRSI---------IIANADSGVGSFADIKGKKMAYGDRA 145
Cdd:pfam16868  45 IQLLRNGEADLAILQSDFAYEAYEGT--GPFAGK--GPLKNLRAItmlypepfqFVVSKDSGIGSIADLKGKRVSVGPPG 120


                  ..
gi 500108775  146 ST 147
Cdd:pfam16868 121 SG 122
PBP2_ThiY_THI5_like cd13564
Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ...
 49-192 2.41e-03

Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway intermediates and similar proteins; the type 2 periplasmic binding protein fold; ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, they 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. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270282 [Multi-domain]  Cd Length: 214  Bit Score: 38.25  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  49 QPLKDYLETTLGKE----------VELIVTTDYSSMIEAMRFGRIDLAYFGPLSYVMAKSKSdiEPFAAMVVDGKPTYRS 118
Cdd:cd13564    9 IPIVYHAPLYLAQQkgyfkeegldVEITTPTGGSDIVQLVASGQFDFGLSAVTHTLVAQSKG--VPVKAVASAIRKPFSG 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500108775 119 IIIAnADSGVGSFADIKGKKMAYgdrasTSSHLIPKTVLLEKAELEAGKDYEAHFVG-SHDAVAVNVANGNADAG 192
Cdd:cd13564   87 VTVL-KDSPIKSPADLKGKKVGY-----NGLKNINETAVRASVRKAGGDPEDVKFVEvGFDQMPAALDSGQIDAA 155
PBP2_Atu4678_like cd13696
The substrate binding domain of putative amino acid transporter; the type 2 periplasmic ...
 55-191 3.00e-03

The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold; This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins 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. 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 receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270414 [Multi-domain]  Cd Length: 227  Bit Score: 38.13  E-value: 3.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  55 LETTLGKEVElIVTTDYSSMIEAMRFGRID--LAYFGPlSYVMAKSKSDIEPF--AAMVVdgkptyrsiiIANADSGVGS 130
Cdd:cd13696   41 LAKALGVKPE-IVETPSPNRIPALVSGRVDvvVANTTR-TLERAKTVAFSIPYvvAGMVV----------LTRKDSGIKS 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500108775 131 FADIKGKKMAyGDRASTSshlipktvllEKAELEAGKDYEAHFVGSHDAVAVNVANGNADA 191
Cdd:cd13696  109 FDDLKGKTVG-VVKGSTN----------EAAVRALLPDAKIQEYDTSADAILALKQGQADA 158
PBP2_ThiY cd13651
Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ...
 60-141 7.59e-03

Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily; ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport , as well as THI5 which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes. After binding the ligand, they 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. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270369 [Multi-domain]  Cd Length: 214  Bit Score: 36.95  E-value: 7.59e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  60 GKEVELIVTTDYSSMIEAMRFGRIDLAyfgpLSY----VMAKSKS-DIEPFAAMVvdgkPTYRSIIIANADSGVGSFADI 134
Cdd:cd13651   30 GLDVEIVAPADPSDPLKLVAAGKADLA----VSYqpqvILARSEGlPVVSVGALV----RSPLNSLMVLKDSGIKSPADL 101


                 ....*..
gi 500108775 135 KGKKMAY 141
Cdd:cd13651  102 KGKKVGY 108
PBP2_TtGluBP cd13567
Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the ...
 95-191 9.34e-03

Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function.


Pssm-ID: 270285 [Multi-domain]  Cd Length: 284  Bit Score: 36.81  E-value: 9.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500108775  95 MAKSKSDIEPFA---AMVVDGKP--TYRSI---------IIANADSGVGSFADIKGKKMAYGdrASTSSHLIPKTVLLEk 160
Cdd:cd13567   55 LALAQNDVAYYAyngTGEFEGKPvkNLRALaalypetvqIVVRADSGIKTVADLKGKRVSVG--APGSGTEVNARQILE- 131

                         90       100       110
                 ....*....|....*....|....*....|....
gi 500108775 161 aelEAGKDY---EAHFVGSHDAVAvNVANGNADA 191
Cdd:cd13567  132 ---AAGLTYddiKVVYLSFAEAAE-ALKDGQIDA 161
 
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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