NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|490279872|ref|WP_004175804|]
View 

MULTISPECIES: ABC transporter substrate-binding protein [Klebsiella]

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
TCDB:  3.A.1

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
14-310 1.76e-43

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


:

Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 151.31  E-value: 1.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  14 LGLMALGGVSLAVQAEEKIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQL 93
Cdd:COG0715    4 LAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEGLDVELVEFAGGAAALEALAAGQADFGVAGAPPA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  94 LEGIQRGFQAKAIAAPFQYDPQGLLTHAD--VTSLQGLKDKTLLVSS-SGQATWWPWLKAQYQL--SDAQVRPYTF--NI 166
Cdd:COG0715   84 LAARAKGAPVKAVAALSQSGGNALVVRKDsgIKSLADLKGKKVAVPGgSTSHYLLRALLAKAGLdpKDVEIVNLPPpdAV 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 167 QPFVVDDAVAQQAYVSSEVfQVQKAGVKANFFLFSEHGYPPYGGILIARPDTIAERKAAMAKFVRASMEGWVSYLKDPAP 246
Cdd:COG0715  164 AALLAGQVDAAVVWEPFES-QAEKKGGGRVLADSADLVPGYPGDVLVASEDFLEENPEAVKAFLRALLKAWAWAAANPDE 242
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490279872 247 GNALIKQDNpKMTDDLLAWGvtqirehhlIDGGDAASQGWGTMTDARWQKTRDFMVSAGLLAAA 310
Cdd:COG0715  243 AAAILAKAT-GLDPEVLAAA---------LEGDLRLDPPLGAPDPARLQRVADFLVELGLLPKD 296
 
Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
14-310 1.76e-43

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 151.31  E-value: 1.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  14 LGLMALGGVSLAVQAEEKIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQL 93
Cdd:COG0715    4 LAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEGLDVELVEFAGGAAALEALAAGQADFGVAGAPPA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  94 LEGIQRGFQAKAIAAPFQYDPQGLLTHAD--VTSLQGLKDKTLLVSS-SGQATWWPWLKAQYQL--SDAQVRPYTF--NI 166
Cdd:COG0715   84 LAARAKGAPVKAVAALSQSGGNALVVRKDsgIKSLADLKGKKVAVPGgSTSHYLLRALLAKAGLdpKDVEIVNLPPpdAV 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 167 QPFVVDDAVAQQAYVSSEVfQVQKAGVKANFFLFSEHGYPPYGGILIARPDTIAERKAAMAKFVRASMEGWVSYLKDPAP 246
Cdd:COG0715  164 AALLAGQVDAAVVWEPFES-QAEKKGGGRVLADSADLVPGYPGDVLVASEDFLEENPEAVKAFLRALLKAWAWAAANPDE 242
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490279872 247 GNALIKQDNpKMTDDLLAWGvtqirehhlIDGGDAASQGWGTMTDARWQKTRDFMVSAGLLAAA 310
Cdd:COG0715  243 AAAILAKAT-GLDPEVLAAA---------LEGDLRLDPPLGAPDPARLQRVADFLVELGLLPKD 296
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
41-244 5.26e-23

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: 94.98  E-value: 5.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872   41 QAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPFQYDPQGLLTH 120
Cdd:pfam09084   1 NPNHAGLYVAQEKGYFKEEGLDVEIVEPADPSDATQLVASGKADFGVSYQESVLLARAKGLPVVSVAALIQHPLSGVISL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  121 AD--VTSLQGLKDKTLLVSSSGQATwwPWLKA---QYQLSDAQVR----PYTFNIQPFVVD--DAVAqQAYVSSEVFQVQ 189
Cdd:pfam09084  81 KDsgIKSPKDLKGKRIGYSGSPFEE--ALLKAllkKDGGDPDDVTivnvGGMNLFPALLTGkvDAAI-GGYYNWEGVELK 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 490279872  190 KAGVKANFFLFSEHGYPPYGGI-LIARPDTIAERKAAMAKFVRASMEGWVSYLKDP 244
Cdd:pfam09084 158 LEGVELNIFALADYGVPDYYSLvLITNEAFLKENPELVRAFLRATLRGYQYALAHP 213
PBP2_ThiY cd13651
Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ...
31-236 2.92e-14

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: 70.46  E-value: 2.92e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  31 KIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPF 110
Cdd:cd13651    1 KVTVLLDWYPNPDHAFLYVAQEKGYFREAGLDVEIVAPADPSDPLKLVAAGKADLAVSYQPQVILARSEGLPVVSVGALV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 111 QYDPQGLLTHAD--VTSLQGLKDKTllVSSSGQATWWPWL-----KAQYQLSDAQVRPYTFNIQPFVVD---DAVAqQAY 180
Cdd:cd13651   81 RSPLNSLMVLKDsgIKSPADLKGKK--VGYSVLGFEEALLdtmlkAAGGDPSDVELVNVGFDLSPALTSgqvDAVI-GAY 157
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490279872 181 VSSEVFQVQKAGVKANFFLFSEHGYPPYGG-ILIARPDTIAERKAAMAKFVRASMEG 236
Cdd:cd13651  158 RNHELNQLAKEGLEGKAFFPEEYGVPNYDElVLVANKDKLPENGEKLRRFLRAAEKG 214
 
Name Accession Description Interval E-value
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
14-310 1.76e-43

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 151.31  E-value: 1.76e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  14 LGLMALGGVSLAVQAEEKIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQL 93
Cdd:COG0715    4 LAALALAACSAAAAAAEKVTLRLGWLPNTDHAPLYVAKEKGYFKKEGLDVELVEFAGGAAALEALAAGQADFGVAGAPPA 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  94 LEGIQRGFQAKAIAAPFQYDPQGLLTHAD--VTSLQGLKDKTLLVSS-SGQATWWPWLKAQYQL--SDAQVRPYTF--NI 166
Cdd:COG0715   84 LAARAKGAPVKAVAALSQSGGNALVVRKDsgIKSLADLKGKKVAVPGgSTSHYLLRALLAKAGLdpKDVEIVNLPPpdAV 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 167 QPFVVDDAVAQQAYVSSEVfQVQKAGVKANFFLFSEHGYPPYGGILIARPDTIAERKAAMAKFVRASMEGWVSYLKDPAP 246
Cdd:COG0715  164 AALLAGQVDAAVVWEPFES-QAEKKGGGRVLADSADLVPGYPGDVLVASEDFLEENPEAVKAFLRALLKAWAWAAANPDE 242
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490279872 247 GNALIKQDNpKMTDDLLAWGvtqirehhlIDGGDAASQGWGTMTDARWQKTRDFMVSAGLLAAA 310
Cdd:COG0715  243 AAAILAKAT-GLDPEVLAAA---------LEGDLRLDPPLGAPDPARLQRVADFLVELGLLPKD 296
NMT1 pfam09084
NMT1/THI5 like; This family contains the NMT1 and THI5 proteins. These proteins are proposed ...
41-244 5.26e-23

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: 94.98  E-value: 5.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872   41 QAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPFQYDPQGLLTH 120
Cdd:pfam09084   1 NPNHAGLYVAQEKGYFKEEGLDVEIVEPADPSDATQLVASGKADFGVSYQESVLLARAKGLPVVSVAALIQHPLSGVISL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  121 AD--VTSLQGLKDKTLLVSSSGQATwwPWLKA---QYQLSDAQVR----PYTFNIQPFVVD--DAVAqQAYVSSEVFQVQ 189
Cdd:pfam09084  81 KDsgIKSPKDLKGKRIGYSGSPFEE--ALLKAllkKDGGDPDDVTivnvGGMNLFPALLTGkvDAAI-GGYYNWEGVELK 157
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 490279872  190 KAGVKANFFLFSEHGYPPYGGI-LIARPDTIAERKAAMAKFVRASMEGWVSYLKDP 244
Cdd:pfam09084 158 LEGVELNIFALADYGVPDYYSLvLITNEAFLKENPELVRAFLRATLRGYQYALAHP 213
PBP2_ThiY cd13651
Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ...
31-236 2.92e-14

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: 70.46  E-value: 2.92e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  31 KIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPF 110
Cdd:cd13651    1 KVTVLLDWYPNPDHAFLYVAQEKGYFREAGLDVEIVAPADPSDPLKLVAAGKADLAVSYQPQVILARSEGLPVVSVGALV 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 111 QYDPQGLLTHAD--VTSLQGLKDKTllVSSSGQATWWPWL-----KAQYQLSDAQVRPYTFNIQPFVVD---DAVAqQAY 180
Cdd:cd13651   81 RSPLNSLMVLKDsgIKSPADLKGKK--VGYSVLGFEEALLdtmlkAAGGDPSDVELVNVGFDLSPALTSgqvDAVI-GAY 157
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490279872 181 VSSEVFQVQKAGVKANFFLFSEHGYPPYGG-ILIARPDTIAERKAAMAKFVRASMEG 236
Cdd:cd13651  158 RNHELNQLAKEGLEGKAFFPEEYGVPNYDElVLVANKDKLPENGEKLRRFLRAAEKG 214
PBP2_NrtA_SsuA_CpmA_like cd01008
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ...
50-236 3.09e-06

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: 47.28  E-value: 3.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  50 AQATGLYKKY--GLDVEIR---SGGPQvngMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAA-PFQYDPQGLLTHAD- 122
Cdd:cd01008   18 AKEKGLFEKEkeGIDVEWVeftSGPPA---LEALAAGSLDFGTGGDTPALLAAAGGVPVVLIAAlSRSPNGNGIVVRKDs 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 123 -VTSLQGLKDKTLLVSSSGqaTWWPWLK---AQYQLSDAQVRPytFNIQPFVVDDAVAQ---QAYVSSEVF--QVQKAGV 193
Cdd:cd01008   95 gITSLADLKGKKIAVTKGT--TGHFLLLkalAKAGLSVDDVEL--VNLGPADAAAALASgdvDAWVTWEPFlsLAEKGGD 170
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 490279872 194 KANFFLFSEHGYPPYGGIlIARPDTIAERKAAMAKFVRASMEG 236
Cdd:cd01008  171 ARIIVDGGGLPYTDPSVL-VARRDFVEENPEAVKALLKALVEA 212
PBP2_SsuA_like_6 cd13563
Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 ...
45-232 8.85e-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: 46.07  E-value: 8.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  45 GGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRAD-VIIGYDlQLLEGIQRGFQAKAIAAP-FQYDPQGLLTHAD 122
Cdd:cd13563   13 GPWYLADEKGFFKKEGLDVELVWFESYSDSMAALASGQIDaAATTLD-DALAMAAKGVPVKIVLVLdNSNGADGIVAKPG 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 123 VTSLQGLKDKTLLVSSSGQATWW-PWLKAQYQLSDAQVRPYTFNI----QPFV---VDDAVAQQAYVSsevfQVQKAGvK 194
Cdd:cd13563   92 IKSIADLKGKTVAVEEGSVSHFLlLNALEKAGLTEKDVKIVNMTAgdagAAFIagqVDAAVTWEPWLS----NALKRG-K 166
                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 490279872 195 ANFFLFSEHGYPPYGGILIARPDTIAERKAAMAKFVRA 232
Cdd:cd13563  167 GKVLVSSADTPGLIPDVLVVREDFIKKNPEAVKAVVKA 204
PBP2_NrtA_CpmA_like cd13553
Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ...
50-235 3.19e-05

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: 44.11  E-value: 3.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  50 AQATGLYKKYGLDVEIR--SGGPQVngMQLLLSKRADVI-IGYDLQLLEGIQRGFQAKAIAApFQYDPQGLLTHADV--T 124
Cdd:cd13553   18 AKEKGFFEKEGLDVELVkfPSWADL--RDALAAGELDAAhVLAPMPAAATYGKGAPIKVVAG-LHRNGSAIVVSKDSgiK 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 125 SLQGLKDKTLLV--SSSGQATWWpwlkaQYQLSDAQVRPYT-FNIQ---PFVVDDAVAQ---QAYVSSEVF--QVQKAGV 193
Cdd:cd13553   95 SVADLKGKTIAVpfPGSTHDVLL-----RYWLAAAGLDPGKdVEIVvlpPPDMVAALAAgqiDAYCVGEPWnaRAVAEGV 169
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490279872 194 kANFFLFSE---HGYPpyGGILIARPDTIAERKAAMAKFVRASME 235
Cdd:cd13553  170 -GRVLADSGdiwPGHP--CCVLVVREDFLEENPEAVQALLKALVE 211
PBP2_DszB cd13554
Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 ...
48-285 1.09e-03

Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 periplasmic binding fold superfamily; This subfamily includes DszB, which converts 2'-hydroxybiphenyl-2-sulfinate to 2-hydroxybiphenyl and sulfinate at the rate-limiting step of the microbial dibenzothiophene desulfurization pathway. The overall fold of DszB is highly similar to those of periplasmic substrate-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. 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. The DszB protein 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. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap.


Pssm-ID: 270272 [Multi-domain]  Cd Length: 246  Bit Score: 39.80  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  48 YQAQATGLYKKYGLDVEIRSGGPQVN-GMQLLLSKRADVIIGYDLQLL--EGIQRGFQAKAIA-APFQYDPQGLLTHAD- 122
Cdd:cd13554   15 LTAEESGYLDAAGIDLEVVAGTPTGTvDFTYDQGIPADVVFSGAIPPLlaEGLRAPGRTRLIGiTPLDLGRQGLFVRADs 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 123 -VTSLQGLKDKTLLVSSSGQATWWpwlKAQYQLSDAQVRPYTFNIQPFVVDDAVAQQAYVSSEV----------FQVQKA 191
Cdd:cd13554   95 pITSAADLEGKRIGMSAGAIRGSW---LARALLHNLEIGGLDVEIVPIDSPGRGQAAALDSGDIdalaswlpwaTTLQAT 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 192 GVKANFFLFSEHGYPPYGGILIARPDTIAERKAAMAKFVRASMEG--WVsylkdpapgnalikQDNPKmtddllawGVTQ 269
Cdd:cd13554  172 GGARPLVDLGLVEGNSYYSTWTVRSDFIEQNPEAVKALVEALVRAgdWI--------------QAHPE--------AVVI 229
                        250
                 ....*....|....*.
gi 490279872 270 IREHHLIDGGDAASQG 285
Cdd:cd13554  230 IHAAEIGVSPGAVGRT 245
PBP2_ThiY_THI5_like cd13564
Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway ...
31-134 1.09e-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: 39.79  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  31 KIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPF 110
Cdd:cd13564    1 TVTVKVGWIPIVYHAPLYLAQQKGYFKEEGLDVEITTPTGGSDIVQLVASGQFDFGLSAVTHTLVAQSKGVPVKAVASAI 80
                         90       100
                 ....*....|....*....|....*.
gi 490279872 111 QYDPQGLLTHAD--VTSLQGLKDKTL 134
Cdd:cd13564   81 RKPFSGVTVLKDspIKSPADLKGKKV 106
PBP2_THI5 cd13650
Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway ...
31-132 6.01e-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: 270368  Cd Length: 251  Bit Score: 37.83  E-value: 6.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  31 KIVLLTSWYAQAEQGGYYQAQATGLYKKYGLDVEIRSGGPQVNGMQLLLSKRADVIIGYDLQLLEGIQRGFQAKAIAAPF 110
Cdd:cd13650    1 KITFLLNWHATPYHIPIFLAQTKGYFKEEGLDVAILEPTNPSDVTELIGSGKVDMGLKAMIHTLAAKARGFPVTSIGSLL 80
                         90       100
                 ....*....|....*....|....*
gi 490279872 111 QYDPQGLLTHAD---VTSLQGLKDK 132
Cdd:cd13650   81 DEPFTGVIYLKGsgiTEDFQSLKGK 105
PBP2_SsuA_like_4 cd13561
Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic ...
48-236 6.38e-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: 37.35  E-value: 6.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872  48 YQAQATGLYKKYGLDVEIR---SGGPQVNGmqlLLSKRADV-IIGYDLQLLeGIQRGFQAKAIAApFQYDPQGLLTHAD- 122
Cdd:cd13561   17 FIAKEKGLFAKHGLDPDFIeftSGPPLVAA---LGSGSLDVgYTGPVAFNL-PASGQAKVVLINN-LENATASLIVRADs 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490279872 123 -VTSLQGLKDKTLLVSSSGQATWWPWL---KAQYQLSDAQVrpytFNIQPFVVDDAVAQQAYVSSEVFQ-----VQKAGV 193
Cdd:cd13561   92 gIASIADLKGKKIGTPSGTTADVALDLalrKAGLSEKDVQI----VNMDPAEIVTAFTSGSVDAAALWApntatIKEKVP 167
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 490279872 194 KANFFLFSEHGYP--PYGGILIARPDTIAERKAAMAKFVRASMEG 236
Cdd:cd13561  168 GAVELADNSDFGPdaAVPGAWVARNKYAEENPEELKKFLAALAEA 212
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH