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Conserved domains on  [gi|2559317380|ref|WP_304673908|]
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ABC transporter substrate-binding protein [Neisseria polysaccharea]

Protein Classification

ABC transporter substrate-binding protein( domain architecture ID 11431285)

ABC transporter substrate-binding protein functions as the initial receptor in the ABC transport of one of a variety of substrates, including ions such as bicarbonate and nitrate; belongs to the type 2 periplasmic binding protein (PBP2) family

CATH:  3.40.190.10
Gene Ontology:  GO:0140359|GO:0042626|GO:0055052
PubMed:  26517916|24638992|25750732
TCDB:  3.A.1

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 9-308 6.89e-31

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


:

Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 117.80  E-value: 6.89e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   9 LKMTAALAAAGVSPSLLAAGKEQFTVYGAPAMPSVTIAVAALQGKLAKQ-ADVSLKIWRSPDQLRAGVASGQFKVMMSPS 87
Cdd:COG0715     1 LAALAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEgLDVELVEFAGGAAALEALAAGQADFGVAGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  88 NVGVNLRNQGQKVGMVNILT--NGITQLMCKGSAITSPQDLVGKKILVPfKNDMPDIVLQALLKKLKIDAHKVSITYAaT 165
Cdd:COG0715    81 PPALAARAKGAPVKAVAALSqsGGNALVVRKDSGIKSLADLKGKKVAVP-GGSTSHYLLRALLAKAGLDPKDVEIVNL-P 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 166 PPEAVGLFLSKDYHAVILPEPMATASLLKGKtmGINVVRGFDLVkawgqvfdtkPLIPMAGIIANEEYFHAHKAQFDIFH 245
Cdd:COG0715   159 PPDAVAALLAGQVDAAVVWEPFESQAEKKGG--GRVLADSADLV----------PGYPGDVLVASEDFLEENPEAVKAFL 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559317380 246 QDLKNALNWILANRQSAAKIGKNYLPAPEPALVMGLDGA-RLTVSKGSEVKNEILKFYEILMQF 308
Cdd:COG0715   227 RALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEGDlRLDPPLGAPDPARLQRVADFLVEL 290
 
Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 9-308 6.89e-31

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 117.80  E-value: 6.89e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   9 LKMTAALAAAGVSPSLLAAGKEQFTVYGAPAMPSVTIAVAALQGKLAKQ-ADVSLKIWRSPDQLRAGVASGQFKVMMSPS 87
Cdd:COG0715     1 LAALAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEgLDVELVEFAGGAAALEALAAGQADFGVAGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  88 NVGVNLRNQGQKVGMVNILT--NGITQLMCKGSAITSPQDLVGKKILVPfKNDMPDIVLQALLKKLKIDAHKVSITYAaT 165
Cdd:COG0715    81 PPALAARAKGAPVKAVAALSqsGGNALVVRKDSGIKSLADLKGKKVAVP-GGSTSHYLLRALLAKAGLDPKDVEIVNL-P 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 166 PPEAVGLFLSKDYHAVILPEPMATASLLKGKtmGINVVRGFDLVkawgqvfdtkPLIPMAGIIANEEYFHAHKAQFDIFH 245
Cdd:COG0715   159 PPDAVAALLAGQVDAAVVWEPFESQAEKKGG--GRVLADSADLV----------PGYPGDVLVASEDFLEENPEAVKAFL 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559317380 246 QDLKNALNWILANRQSAAKIGKNYLPAPEPALVMGLDGA-RLTVSKGSEVKNEILKFYEILMQF 308
Cdd:COG0715   227 RALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEGDlRLDPPLGAPDPARLQRVADFLVEL 290
PBP2_ThiY_THI5_like_1 cd13652
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ...
 42-195 1.55e-12

Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold; This subfamily is phylogenetically similar to ThiY, which 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: 270370 [Multi-domain]  Cd Length: 217  Bit Score: 65.87  E-value: 1.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  42 SVTIAVAALQGKLAKQA-DVSLKIWRSPDQLRAGVASGQFKV-MMSPSNVGVNLRNQGQKVGMVNILTN-----GITQLM 114
Cdd:cd13652    14 FAPVYIAAEKGYFKEEGlDVEITRFASGAEILAALASGQVDVaGSSPGASLLGALARGADLKIVAEGLGttpgyGPFAIV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 115 C-KGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKKLKIDAHKVSITYAAtPPEAVGLFLSKDYHAVILPEPMATASLL 193
Cdd:cd13652    94 VrADSGITSPADLVGKKIAVSTLTNILEYTTNAYLKKNGLDPDKVEFVEVA-FPQMVPALENGNVDAAVLAEPFLSRARS 172


                  ..
gi 2559317380 194 KG 195
Cdd:cd13652   173 SG 174
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
 100-299 1.29e-08

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: 55.06  E-value: 1.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 100 VGMVNIlTNGITQLMCKGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKK-LKIDAhkVSITYAAtPPEAVGLFLSKDY 178
Cdd:TIGR01728  74 VGLVSD-NKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAgLSGDD--VTILYLG-PSDARAAFAAGQV 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 179 HAVILPEPMATASLLKGKTMginvvrgfdLVKAWGQVFDTkplIPMAGIIANEEYFHAHKAQFDIFHQDLKNALNWILAN 258
Cdd:TIGR01728 150 DAWAIWEPWGSALVEEGGAR---------VLANGEGIGLP---GQPGFLVVRREFAEAHPEQVQRVLKVLVKARKWAEEN 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2559317380 259 RQSAAKIGKNYLPAPEPALvmgldgaRLTVSKGSEVKNEIL 299
Cdd:TIGR01728 218 PEESAKILAKELGLSQAVV-------EETVLNRRFLRVEVI 251
TAT_signal pfam10518
TAT (twin-arginine translocation) pathway signal sequence;
2-27 1.45e-03

TAT (twin-arginine translocation) pathway signal sequence;


Pssm-ID: 463131 [Multi-domain]  Cd Length: 26  Bit Score: 35.43  E-value: 1.45e-03
                          10        20
                  ....*....|....*....|....*.
gi 2559317380   2 DMKRRDFLKMTAALAAAGVSPSLLAA 27
Cdd:pfam10518   1 KLSRRDFLKGSAAAAAAAALGGCAAA 26
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 54-196 2.50e-03

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 38.46  E-value: 2.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   54 LAKQADVSLK-IWRSPDQLRAGVASGQFKVMMSPSNVGVNLRNQgqkvgmVNI----LTNGITQLMCKGSAITSPQDLVG 128
Cdd:smart00062  33 IAKELGLKVEfVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQ------VDFsdpyYRSGQVILVRKDSPIKSLEDLKG 106

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2559317380  129 KKILVpfkndMPDIVLQALLKKLkidAHKVSITYAATPPEAVGLFLSKDYHAVILPEPMATASLLKGK 196
Cdd:smart00062 107 KKVAV-----VAGTTAEELLKKL---YPEAKIVSYDSNAEALAALKAGRADAAVADAPLLAALVKQHG 166
 
Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
 9-308 6.89e-31

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 117.80  E-value: 6.89e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   9 LKMTAALAAAGVSPSLLAAGKEQFTVYGAPAMPSVTIAVAALQGKLAKQ-ADVSLKIWRSPDQLRAGVASGQFKVMMSPS 87
Cdd:COG0715     1 LAALAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEgLDVELVEFAGGAAALEALAAGQADFGVAGA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  88 NVGVNLRNQGQKVGMVNILT--NGITQLMCKGSAITSPQDLVGKKILVPfKNDMPDIVLQALLKKLKIDAHKVSITYAaT 165
Cdd:COG0715    81 PPALAARAKGAPVKAVAALSqsGGNALVVRKDSGIKSLADLKGKKVAVP-GGSTSHYLLRALLAKAGLDPKDVEIVNL-P 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 166 PPEAVGLFLSKDYHAVILPEPMATASLLKGKtmGINVVRGFDLVkawgqvfdtkPLIPMAGIIANEEYFHAHKAQFDIFH 245
Cdd:COG0715   159 PPDAVAALLAGQVDAAVVWEPFESQAEKKGG--GRVLADSADLV----------PGYPGDVLVASEDFLEENPEAVKAFL 226

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2559317380 246 QDLKNALNWILANRQSAAKIGKNYLPAPEPALVMGLDGA-RLTVSKGSEVKNEILKFYEILMQF 308
Cdd:COG0715   227 RALLKAWAWAAANPDEAAAILAKATGLDPEVLAAALEGDlRLDPPLGAPDPARLQRVADFLVEL 290
PBP2_ThiY_THI5_like_1 cd13652
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ...
 42-195 1.55e-12

Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold; This subfamily is phylogenetically similar to ThiY, which 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: 270370 [Multi-domain]  Cd Length: 217  Bit Score: 65.87  E-value: 1.55e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  42 SVTIAVAALQGKLAKQA-DVSLKIWRSPDQLRAGVASGQFKV-MMSPSNVGVNLRNQGQKVGMVNILTN-----GITQLM 114
Cdd:cd13652    14 FAPVYIAAEKGYFKEEGlDVEITRFASGAEILAALASGQVDVaGSSPGASLLGALARGADLKIVAEGLGttpgyGPFAIV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 115 C-KGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKKLKIDAHKVSITYAAtPPEAVGLFLSKDYHAVILPEPMATASLL 193
Cdd:cd13652    94 VrADSGITSPADLVGKKIAVSTLTNILEYTTNAYLKKNGLDPDKVEFVEVA-FPQMVPALENGNVDAAVLAEPFLSRARS 172


                  ..
gi 2559317380 194 KG 195
Cdd:cd13652   173 SG 174
PBP2_NrtA_CpmA_like cd13553
Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ...
 38-196 1.02e-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: 57.59  E-value: 1.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  38 PAMPSVTIAVAALQGKLAKQA-DVSLKIWRSPDQLRAGVASGQFKV--MMSPSNVGVNLRNQGQ-KVGMVNIlTNGITQL 113
Cdd:cd13553     8 PITDHAPLLVAKEKGFFEKEGlDVELVKFPSWADLRDALAAGELDAahVLAPMPAAATYGKGAPiKVVAGLH-RNGSAIV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 114 MCKGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKKLKIDAHK-VSITYAAtPPEAVGLFLSKDYHAVILPEPMATASL 192
Cdd:cd13553    87 VSKDSGIKSVADLKGKTIAVPFPGSTHDVLLRYWLAAAGLDPGKdVEIVVLP-PPDMVAALAAGQIDAYCVGEPWNARAV 165


                  ....
gi 2559317380 193 LKGK 196
Cdd:cd13553   166 AEGV 169
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
 100-299 1.29e-08

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: 55.06  E-value: 1.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 100 VGMVNIlTNGITQLMCKGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKK-LKIDAhkVSITYAAtPPEAVGLFLSKDY 178
Cdd:TIGR01728  74 VGLVSD-NKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAgLSGDD--VTILYLG-PSDARAAFAAGQV 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 179 HAVILPEPMATASLLKGKTMginvvrgfdLVKAWGQVFDTkplIPMAGIIANEEYFHAHKAQFDIFHQDLKNALNWILAN 258
Cdd:TIGR01728 150 DAWAIWEPWGSALVEEGGAR---------VLANGEGIGLP---GQPGFLVVRREFAEAHPEQVQRVLKVLVKARKWAEEN 217

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 2559317380 259 RQSAAKIGKNYLPAPEPALvmgldgaRLTVSKGSEVKNEIL 299
Cdd:TIGR01728 218 PEESAKILAKELGLSQAVV-------EETVLNRRFLRVEVI 251
TauA COG4521
ABC-type taurine transport system, periplasmic component [Inorganic ion transport and ...
 4-160 9.87e-08

ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism];


Pssm-ID: 443595 [Multi-domain]  Cd Length: 332  Bit Score: 52.57  E-value: 9.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   4 KRRDFLKMTAALAAAGVSPSLLAAGKEqFTV-YGAPAMPSVtiaVAALQGKLAKQADVSLKiWRS----PDQLRAgVASG 78
Cdd:COG4521     3 FKRLLLLAALALAGCALAAAAAAAAKE-VTIgYQTIPNPEL---VAKADGALEKALGAKVN-WRKfdsgADVITA-LASG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  79 QFKVM---MSPSNVGVNlrnQGQKVGMVNILTNGITQLMC---KGSAITSPQDLVGKKILVPFkNDMPDIVLQALLKKLK 152
Cdd:COG4521    77 DVDIGsigSSPFAAALS---RGLPIEVIWIADVIGDAEALvvrNGSGITSPKDLKGKKIAVPF-GSTSHYSLLAALKHAG 152


                  ....*...
gi 2559317380 153 IDAHKVSI 160
Cdd:COG4521   153 IDPSDVTI 160
PBP2_ThiY_THI5_like cd13564
Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ...
 29-159 3.62e-06

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: 47.11  E-value: 3.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  29 KEQFTVYGAPAMPSVTIAVAALQGKLAKQA-DVSLKIWRSPDQLRAGVASGQFKVMMSPSNVGVNLRNQGQKVGMVNILT 107
Cdd:cd13564     1 TVTVKVGWIPIVYHAPLYLAQQKGYFKEEGlDVEITTPTGGSDIVQLVASGQFDFGLSAVTHTLVAQSKGVPVKAVASAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2559317380 108 ----NGITQLmcKGSAITSPQDLVGKKILVPFKNDMPDIVLQALLKKLKIDAHKVS 159
Cdd:cd13564    81 rkpfSGVTVL--KDSPIKSPADLKGKKVGYNGLKNINETAVRASVRKAGGDPEDVK 134
PBP2_SsuA_like_4 cd13561
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ...
 35-198 1.12e-05

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: 45.44  E-value: 1.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  35 YGAPAMPSVTIAVAALQGKLAKQA-DVSLKIWRSPDQLRAGVASGQFKVMM---SPSNVGVNLrnqGQKVGMVNILTNGI 110
Cdd:cd13561     6 YLPALAVAGPIFIAKEKGLFAKHGlDPDFIEFTSGPPLVAALGSGSLDVGYtgpVAFNLPASG---QAKVVLINNLENAT 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 111 TQL-MCKGSAITSPQDLVGKKILVPfKNDMPDIVLQALLKKLKIDAHKVSITYAAtPPEAVGLFLSKDYHAVILPEPMAT 189
Cdd:cd13561    83 ASLiVRADSGIASIADLKGKKIGTP-SGTTADVALDLALRKAGLSEKDVQIVNMD-PAEIVTAFTSGSVDAAALWAPNTA 160


                  ....*....
gi 2559317380 190 ASLLKGKTM 198
Cdd:cd13561   161 TIKEKVPGA 169
HisJ COG0834
ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino ...
 54-275 4.90e-05

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: 43.82  E-value: 4.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  54 LAKQADVSLKI-WRSPDQLRAGVASGQFKVMMSpsNVGVNLRNQgQKVGMVNILTNGITQLMCK--GSAITSPQDLVGKK 130
Cdd:COG0834    32 IAKRLGLKVEFvPVPWDRLIPALQSGKVDLIIA--GMTITPERE-KQVDFSDPYYTSGQVLLVRkdNSGIKSLADLKGKT 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 131 ILVPfKNDMPDIVLQALLKKLKidahkvsITYAATPPEAVGLFLSKDYHAVILPEPMATASLLKGKTMGINVVrgfdlvk 210
Cdd:COG0834   109 VGVQ-AGTTYEEYLKKLGPNAE-------IVEFDSYAEALQALASGRVDAVVTDEPVAAYLLAKNPGDDLKIV------- 173

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2559317380 211 awGQVFDTKPLipmaGIIANEEyfhahkaqfdifHQDLKNALNWILANRQ---SAAKIGKNYLPAPEP 275
Cdd:COG0834   174 --GEPLSGEPY----GIAVRKG------------DPELLEAVNKALAALKadgTLDKILEKWFGEDVP 223
PBP2_taurine cd13560
Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold; This ...
 116-198 5.51e-04

Taurine-binding periplasmic 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: 270278 [Multi-domain]  Cd Length: 218  Bit Score: 40.75  E-value: 5.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 116 KGSAITSPQDLVGKKILVPFkNDMPDIVLQALLKKLKIDAHKVSItYAATPPEAVGLFLSKDYHAVILPEPmATASLLK- 194
Cdd:cd13560    89 KGSGIKSLKDLAGKKVAVPF-GSTAHYSLLAALKHAGVDPGKVKI-LDMQPPEIVAAWQRGDIDAAYVWEP-ALSQLKKn 165


                  ....
gi 2559317380 195 GKTM 198
Cdd:cd13560   166 GKVL 169
TAT_signal pfam10518
TAT (twin-arginine translocation) pathway signal sequence;
2-27 1.45e-03

TAT (twin-arginine translocation) pathway signal sequence;


Pssm-ID: 463131 [Multi-domain]  Cd Length: 26  Bit Score: 35.43  E-value: 1.45e-03
                          10        20
                  ....*....|....*....|....*.
gi 2559317380   2 DMKRRDFLKMTAALAAAGVSPSLLAA 27
Cdd:pfam10518   1 KLSRRDFLKGSAAAAAAAALGGCAAA 26
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
 54-196 2.50e-03

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


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 38.46  E-value: 2.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380   54 LAKQADVSLK-IWRSPDQLRAGVASGQFKVMMSPSNVGVNLRNQgqkvgmVNI----LTNGITQLMCKGSAITSPQDLVG 128
Cdd:smart00062  33 IAKELGLKVEfVEVSFDSLLTALKSGKIDVVAAGMTITPERAKQ------VDFsdpyYRSGQVILVRKDSPIKSLEDLKG 106

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2559317380  129 KKILVpfkndMPDIVLQALLKKLkidAHKVSITYAATPPEAVGLFLSKDYHAVILPEPMATASLLKGK 196
Cdd:smart00062 107 KKVAV-----VAGTTAEELLKKL---YPEAKIVSYDSNAEALAALKAGRADAAVADAPLLAALVKQHG 166
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
 107-262 2.93e-03

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: 38.36  E-value: 2.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 107 TNGITQLmcKGSAITSPQDLVGKKI-LVPFKNDmpDIVLQALLKKLKIDAhkvsityaatppeavglflsKDYHAVILPE 185
Cdd:pfam09084  74 LSGVISL--KDSGIKSPKDLKGKRIgYSGSPFE--EALLKALLKKDGGDP--------------------DDVTIVNVGG 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380 186 PMATASLLKGKT-MGINVVRGFDLVKAWGQVFDTK---------PLIPMAGIIANEEYFHAHKAQFDIFHQDLKNALNWI 255
Cdd:pfam09084 130 MNLFPALLTGKVdAAIGGYYNWEGVELKLEGVELNifaladygvPDYYSLVLITNEAFLKENPELVRAFLRATLRGYQYA 209


                  ....*..
gi 2559317380 256 LANRQSA 262
Cdd:pfam09084 210 LAHPEEA 216
PBP2_MidA_like cd01004
Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 ...
 54-172 3.62e-03

Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold; This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding domain 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 two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis.


Pssm-ID: 270225 [Multi-domain]  Cd Length: 230  Bit Score: 38.38  E-value: 3.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2559317380  54 LAKQADVSLKIWRSP-DQLRAGVASGQFKVMMspSNVGVNLRNQgQKVGMVNILTNGITQLMCKGS--AITSPQDLVGKK 130
Cdd:cd01004    35 IAKRLGLKVEIVNVSfDGLIPALQSGRYDIIM--SGITDTPERA-KQVDFVDYMKDGLGVLVAKGNpkKIKSPEDLCGKT 111

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2559317380 131 ILVPfKNDMPDIVLQALLKKLKiDAHKVSITYAATPPEAVGL 172
Cdd:cd01004   112 VAVQ-TGTTQEQLLQAANKKCK-AAGKPAIEIQTFPDQADAL 151
COG4102 COG4102
Uncharacterized conserved protein, DUF1501 family [Function unknown];
3-27 5.66e-03

Uncharacterized conserved protein, DUF1501 family [Function unknown];


Pssm-ID: 443278  Cd Length: 395  Bit Score: 38.00  E-value: 5.66e-03
                          10        20
                  ....*....|....*....|....*.
gi 2559317380   3 MKRRDFLKMTAALAAAGVS-PSLLAA 27
Cdd:COG4102     1 LSRRDFLKASAAAGAGGLAlPGLLAA 26
 
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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