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Conserved domains on  [gi|497532543|ref|WP_009846741|]
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MULTISPECIES: substrate-binding domain-containing protein [Vibrio]

Protein Classification

TupB family protein( domain architecture ID 10006838)

TupB family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TupB COG2998
ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and ...
 2-268 7.15e-162

ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and metabolism];


:

Pssm-ID: 442236  Cd Length: 272  Bit Score: 449.62  E-value: 7.15e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   2 KAIPLTIAALSIVSYTASSAEDTTHIKLATTTSTYHSGLLDYLLPEFEKDSGIKVDVLAAGTGKSLRMGENGDVDLVMTH 81
Cdd:COG2998    4 RLLLLLLLLLLALALAGAAAAAAESLRLATTTSTEDSGLLDYLLPAFEKKTGIEVKVVAVGTGQALELGRRGDADVLLVH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  82 APKAEANFVEKGYGVLPRKLMYNDFVIVGPQSDPAKIESQKAVADVFKAIANNNVTFVSRGDDSGTHKKEMGIWAQTKME 161
Cdd:COG2998   84 APSAEEKFVAEGYGVNRRDVMYNDFVIVGPADDPAGIKGAKDAAEALKKIAEAKAPFVSRGDDSGTHKKELRLWKAAGID 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543 162 PNFGGYRSVGQGMGPTLNMASEMQGYTMTDRGTWLAYQNKLDLKVLFQGDKNLFNPYQVILVNPERYPSINYQAAKVFSD 241
Cdd:COG2998  164 PSGDWYRETGQGMGATLNMAAEKGAYTLTDRGTYLAFKNKLDLEILVEGDPRLFNQYGVIAVNPEKHPHVNYELAQAFID 243

                        250       260
                 ....*....|....*....|....*..
gi 497532543 242 WLVNPKGQKLINDFKLHGKQLFVANAE 268
Cdd:COG2998  244 WLTSPEGQKIIASFGVDGEPLFFPNAG 270
 
Name Accession Description Interval E-value
TupB COG2998
ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and ...
 2-268 7.15e-162

ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and metabolism];


Pssm-ID: 442236  Cd Length: 272  Bit Score: 449.62  E-value: 7.15e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   2 KAIPLTIAALSIVSYTASSAEDTTHIKLATTTSTYHSGLLDYLLPEFEKDSGIKVDVLAAGTGKSLRMGENGDVDLVMTH 81
Cdd:COG2998    4 RLLLLLLLLLLALALAGAAAAAAESLRLATTTSTEDSGLLDYLLPAFEKKTGIEVKVVAVGTGQALELGRRGDADVLLVH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  82 APKAEANFVEKGYGVLPRKLMYNDFVIVGPQSDPAKIESQKAVADVFKAIANNNVTFVSRGDDSGTHKKEMGIWAQTKME 161
Cdd:COG2998   84 APSAEEKFVAEGYGVNRRDVMYNDFVIVGPADDPAGIKGAKDAAEALKKIAEAKAPFVSRGDDSGTHKKELRLWKAAGID 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543 162 PNFGGYRSVGQGMGPTLNMASEMQGYTMTDRGTWLAYQNKLDLKVLFQGDKNLFNPYQVILVNPERYPSINYQAAKVFSD 241
Cdd:COG2998  164 PSGDWYRETGQGMGATLNMAAEKGAYTLTDRGTYLAFKNKLDLEILVEGDPRLFNQYGVIAVNPEKHPHVNYELAQAFID 243

                        250       260
                 ....*....|....*....|....*..
gi 497532543 242 WLVNPKGQKLINDFKLHGKQLFVANAE 268
Cdd:COG2998  244 WLTSPEGQKIIASFGVDGEPLFFPNAG 270
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 17-247 2.04e-39

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 138.06  E-value: 2.04e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   17 TASSAEDTTHIKLATTTSTYHSGLLDYLLPEFEKDSGIKVDVLAAGTGKSLRMGENGDVDLVMTHAPKAEANFVE----K 92
Cdd:pfam12849   1 SAAASAPTVGTILIAGSSTQAPGLLDLAEAFEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALVSRPLTEEEFEAfganG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   93 GYGVLPRKLMYNDFVIVGPQSDPAKIESQKAVADVFKAIANN--------NVTFVSRGDDSGT------HKKEMGIWAQT 158
Cdd:pfam12849  81 AGGLVEVPVAYDGIAIVVNKDNPANILTVEALKKIFSGKITNwndggpdgPIKFVSRGDNSGTtelfstHLKEKGPWGAA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  159 KMEPNFGG---YRSVGQGMGPTLNMASEM--QGYTMTD--RGTWLAYQNKLDLKVLF--------------QGDKNLFNP 217
Cdd:pfam12849 161 GIGAAGSPgvaSVVAGPGAIGYVEVSYALanLGYTLADvaGGTYLSFAKALKVAKINpgaglvipleeaiaDGDYPLSRP 240

                         250       260       270
                  ....*....|....*....|....*....|
gi 497532543  218 YQVILVNPERYPSinyQAAKVFSDWLVNPK 247
Cdd:pfam12849 241 YYVIVKNPPKGPA---PLAKAFLDFLLSDE 267
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 26-163 3.54e-03

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 37.58  E-value: 3.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  26 HIKLATTTSTYHSGLLDyLLPEFEKDS-GIKVDVLAAGTGKSLRMGENGDVDLVMTHAPKAEANFVekgygVLPrkLMYN 104
Cdd:cd05466    1 TLRIGASPSIAAYLLPP-LLAAFRQRYpGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLE-----SEP--LFEE 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 497532543 105 DFVIVGPQSDPAKIESQKAVADVfkaianNNVTFVSRGDDSGTHKKEMGIWAQTKMEPN 163
Cdd:cd05466   73 PLVLVVPPDHPLAKRKSVTLADL------ADEPLILFERGSGLRRLLDRAFAEAGFTPN 125
 
Name Accession Description Interval E-value
TupB COG2998
ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and ...
 2-268 7.15e-162

ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and metabolism];


Pssm-ID: 442236  Cd Length: 272  Bit Score: 449.62  E-value: 7.15e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   2 KAIPLTIAALSIVSYTASSAEDTTHIKLATTTSTYHSGLLDYLLPEFEKDSGIKVDVLAAGTGKSLRMGENGDVDLVMTH 81
Cdd:COG2998    4 RLLLLLLLLLLALALAGAAAAAAESLRLATTTSTEDSGLLDYLLPAFEKKTGIEVKVVAVGTGQALELGRRGDADVLLVH 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  82 APKAEANFVEKGYGVLPRKLMYNDFVIVGPQSDPAKIESQKAVADVFKAIANNNVTFVSRGDDSGTHKKEMGIWAQTKME 161
Cdd:COG2998   84 APSAEEKFVAEGYGVNRRDVMYNDFVIVGPADDPAGIKGAKDAAEALKKIAEAKAPFVSRGDDSGTHKKELRLWKAAGID 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543 162 PNFGGYRSVGQGMGPTLNMASEMQGYTMTDRGTWLAYQNKLDLKVLFQGDKNLFNPYQVILVNPERYPSINYQAAKVFSD 241
Cdd:COG2998  164 PSGDWYRETGQGMGATLNMAAEKGAYTLTDRGTYLAFKNKLDLEILVEGDPRLFNQYGVIAVNPEKHPHVNYELAQAFID 243

                        250       260
                 ....*....|....*....|....*..
gi 497532543 242 WLVNPKGQKLINDFKLHGKQLFVANAE 268
Cdd:COG2998  244 WLTSPEGQKIIASFGVDGEPLFFPNAG 270
PBP_like_2 pfam12849
PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.
 17-247 2.04e-39

PBP superfamily domain; This domain belongs to the periplasmic binding protein superfamily.


Pssm-ID: 432831 [Multi-domain]  Cd Length: 267  Bit Score: 138.06  E-value: 2.04e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   17 TASSAEDTTHIKLATTTSTYHSGLLDYLLPEFEKDSGIKVDVLAAGTGKSLRMGENGDVDLVMTHAPKAEANFVE----K 92
Cdd:pfam12849   1 SAAASAPTVGTILIAGSSTQAPGLLDLAEAFEKKYPGAKVKVTSVGSGEGIKALLNGDVDVALVSRPLTEEEFEAfganG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   93 GYGVLPRKLMYNDFVIVGPQSDPAKIESQKAVADVFKAIANN--------NVTFVSRGDDSGT------HKKEMGIWAQT 158
Cdd:pfam12849  81 AGGLVEVPVAYDGIAIVVNKDNPANILTVEALKKIFSGKITNwndggpdgPIKFVSRGDNSGTtelfstHLKEKGPWGAA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  159 KMEPNFGG---YRSVGQGMGPTLNMASEM--QGYTMTD--RGTWLAYQNKLDLKVLF--------------QGDKNLFNP 217
Cdd:pfam12849 161 GIGAAGSPgvaSVVAGPGAIGYVEVSYALanLGYTLADvaGGTYLSFAKALKVAKINpgaglvipleeaiaDGDYPLSRP 240

                         250       260       270
                  ....*....|....*....|....*....|
gi 497532543  218 YQVILVNPERYPSinyQAAKVFSDWLVNPK 247
Cdd:pfam12849 241 YYVIVKNPPKGPA---PLAKAFLDFLLSDE 267
SBP_bac_11 pfam13531
Bacterial extracellular solute-binding protein; This family includes bacterial extracellular ...
 44-126 5.44e-06

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


Pssm-ID: 463911 [Multi-domain]  Cd Length: 225  Bit Score: 46.10  E-value: 5.44e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   44 LLPEFEKDSGIKVDVLAAGTGKSLRMGENG-DVDLVMTHAPKAEANFVEKGYGVL--PRKLMYNDFVIVGPQSDPAKIES 120
Cdd:pfam13531  15 LAAAFEAETGVKVVVSYGGSGKLAKQIANGaPADVFISADSAWLDKLAAAGLVVPgsRVPLAYSPLVIAVPKGNPKDISG 94


                  ....*.
gi 497532543  121 QKAVAD 126
Cdd:pfam13531  95 LADLLK 100
ModA COG0725
ABC-type molybdate transport system, periplasmic Mo-binding protein ModA [Inorganic ion ...
 6-133 3.19e-04

ABC-type molybdate transport system, periplasmic Mo-binding protein ModA [Inorganic ion transport and metabolism]; ABC-type molybdate transport system, periplasmic Mo-binding protein ModA is part of the Pathway/BioSystem: Molybdopterin biosynthesis


Pssm-ID: 440489 [Multi-domain]  Cd Length: 253  Bit Score: 41.01  E-value: 3.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543   6 LTIAALSIVSYTASSAEDTthIKLATTTSTyhSGLLDYLLPEFEKDS-GIKVDVLAAGTGKSLRMGENG-DVDLVMTHAP 83
Cdd:COG0725    8 LLLLALLLAGASAAAAAAE--LTVFAAASL--KEALEELAAAFEKEHpGVKVELSFGGSGALARQIEQGaPADVFISADE 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 497532543  84 K-----AEANFVEKGYgvlPRKLMYNDFVIVGPQSDPAKIESQKAVADV-FK-AIAN 133
Cdd:COG0725   84 KymdklAKKGLILAGS---RVVFATNRLVLAVPKGNPADISSLEDLAKPgVRiAIGD 137
PBP2_LTTR_substrate cd05466
The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the ...
 26-163 3.54e-03

The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily; This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 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 cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction.


Pssm-ID: 176102 [Multi-domain]  Cd Length: 197  Bit Score: 37.58  E-value: 3.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  26 HIKLATTTSTYHSGLLDyLLPEFEKDS-GIKVDVLAAGTGKSLRMGENGDVDLVMTHAPKAEANFVekgygVLPrkLMYN 104
Cdd:cd05466    1 TLRIGASPSIAAYLLPP-LLAAFRQRYpGVELSLVEGGSSELLEALLEGELDLAIVALPVDDPGLE-----SEP--LFEE 72

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 497532543 105 DFVIVGPQSDPAKIESQKAVADVfkaianNNVTFVSRGDDSGTHKKEMGIWAQTKMEPN 163
Cdd:cd05466   73 PLVLVVPPDHPLAKRKSVTLADL------ADEPLILFERGSGLRRLLDRAFAEAGFTPN 125
PBP2_FutA1_ilke cd13542
Substrate binding domain of ferric iron-binding protein, a member of the type 2 periplasmic ...
 34-80 5.45e-03

Substrate binding domain of ferric iron-binding protein, a member of the type 2 periplasmic binding fold superfamily; FutA1 is the periplasmic component of an ABC-type iron transporter and serves as the primary receptor in Synerchosystis species. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria and is critical for survival of these pathogens within the host. After binding iron with high affinity, FutA1 interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 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: 270260 [Multi-domain]  Cd Length: 314  Bit Score: 37.70  E-value: 5.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 497532543  34 STYHSGLLDYLLPEFEKDSGIKVD-VLAAGTGKSLRM---GENGDVDLVMT 80
Cdd:cd13542    6 SSRHYNTDKPLYKAFEKETGIKVNvVFASADELLERLkaeGANSPADVLLT 56
PstS COG0226
ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and ...
 47-148 6.04e-03

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


Pssm-ID: 439996 [Multi-domain]  Cd Length: 275  Bit Score: 37.17  E-value: 6.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497532543  47 EFEK-DSGIKVDVLAAGTGKSLRMGENGDVDLVMTHAP-KAE--ANFVEKGYGVLPRKLMYNDFVIVGPQSDPAKIESQK 122
Cdd:COG0226   24 AFQKaNPGVTINVQSGGSGGGIKQFIAGTVDIGNSSRPlKDEelEAAKENGVELVEIPVAIDGIAVVVNPDNPVKNLTGE 103

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 497532543 123 AVADVFK-----------AIANNNVTFVSRGDDSGTH 148
Cdd:COG0226  104 QLADIFSgkitnwndiggKLPDEPITVVGRSDGSGTT 140
 
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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