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Conserved domains on  [gi|257780973|gb|ACV64867|]
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protein of unknown function DUF191 [Desulfofarcimen acetoxidans DSM 771]

Protein Classification

1,4-dihydroxy-6-naphthoate synthase( domain architecture ID 10194533)

1,4-dihydroxy-6-naphthoate synthase catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PBP2_Ttha1568_Mqnd cd13635
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
1-264 5.58e-127

A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ttha1568 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. 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.


:

Pssm-ID: 270353  Cd Length: 260  Bit Score: 361.45  E-value: 5.58e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   1 MKIVFSPCPNDTFIFHAWVHGLVPGAP-ELDVALADIDVTNKLAAGpNGPDIIKISFAALPWVLSKYALLPCGGALGRGC 79
Cdd:cd13635    2 LSLGISPCPNDTFIFGALLHGLIDTPGlTFDVFLADVETLNRLALE-GRLDVTKLSFAALPHLLDDYALLRSGGALGRGC 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVlVANKPCGIinpADLAGRRVAVPAERSTAYLLFRLWLdqhvpGGVGEIIILPFHEIMPAVRDGLVDAGLVIHESRF 159
Cdd:cd13635   81 GPLL-VARKPDSI---EDLRGKRIAIPGENTTAHLLLRLFY-----PDDFELVPMRFDEIMPAVLRGEVDAGVIIHEGRF 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 160 TYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLD---LSAITGWLRESVKYAWAHPEASQEYVLRHAQELSPEVAKA 236
Cdd:cd13635  152 TYQDYGLHKLLDLGEWWEEETGLPIPLGGIVIRRDLGaalARAIEEAIRRSLEYARAHPEAARPYIREHAQELDDEVIRQ 231
                        250       260
                 ....*....|....*....|....*....
gi 257780973 237 HIRLYVNEFTLNLG-EGYGAVISLLSRAA 264
Cdd:cd13635  232 HIDLYVNEFSLDLGeEGRAAVATLLERAE 260
 
Name Accession Description Interval E-value
PBP2_Ttha1568_Mqnd cd13635
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
1-264 5.58e-127

A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ttha1568 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. 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.


Pssm-ID: 270353  Cd Length: 260  Bit Score: 361.45  E-value: 5.58e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   1 MKIVFSPCPNDTFIFHAWVHGLVPGAP-ELDVALADIDVTNKLAAGpNGPDIIKISFAALPWVLSKYALLPCGGALGRGC 79
Cdd:cd13635    2 LSLGISPCPNDTFIFGALLHGLIDTPGlTFDVFLADVETLNRLALE-GRLDVTKLSFAALPHLLDDYALLRSGGALGRGC 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVlVANKPCGIinpADLAGRRVAVPAERSTAYLLFRLWLdqhvpGGVGEIIILPFHEIMPAVRDGLVDAGLVIHESRF 159
Cdd:cd13635   81 GPLL-VARKPDSI---EDLRGKRIAIPGENTTAHLLLRLFY-----PDDFELVPMRFDEIMPAVLRGEVDAGVIIHEGRF 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 160 TYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLD---LSAITGWLRESVKYAWAHPEASQEYVLRHAQELSPEVAKA 236
Cdd:cd13635  152 TYQDYGLHKLLDLGEWWEEETGLPIPLGGIVIRRDLGaalARAIEEAIRRSLEYARAHPEAARPYIREHAQELDDEVIRQ 231
                        250       260
                 ....*....|....*....|....*....
gi 257780973 237 HIRLYVNEFTLNLG-EGYGAVISLLSRAA 264
Cdd:cd13635  232 HIDLYVNEFSLDLGeEGRAAVATLLERAE 260
MqnD COG2107
1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme ...
1-273 2.15e-124

1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; 1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis


Pssm-ID: 441710  Cd Length: 276  Bit Score: 355.60  E-value: 2.15e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   1 MKIVFSPCPNDTFIFHAWVHGLVP-GAPELDVALADIDVTNKLAAgpNGP-DIIKISFAALPWVLSKYALLPCGGALGRG 78
Cdd:COG2107    4 ITLGHSPDPDDAFMFYALAHGKVDtEGFEFEHVLEDIETLNRRAL--KGElDVTAISFHAYPYIADDYALLRSGASLGRG 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  79 CGPLVlVANKPcgiINPADLAGRRVAVPAERSTAYLLFRLWLdqhvpGGVGEIIILPFHEIMPAVRDGLVDAGLVIHESR 158
Cdd:COG2107   82 YGPLV-VAKKP---MSLEELKGKRIAVPGRYTTAYLLLRLAL-----PKAFEVVEMPFDEIMPAVLSGEVDAGLIIHEGQ 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 159 FTYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLDLSAITGW---LRESVKYAWAHPEASQEYVLRHAQELSPEVAK 235
Cdd:COG2107  153 LTYAEYGLVKVLDLGEWWEEETGLPLPLGGNVIRRDLGEEVARKIeeaLRKSIKYALAHPDEALEYAMKYARELDEEVID 232
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 257780973 236 AHIRLYVNEFTLNLGE-GYGAVISLLSRAAQAGLIPDVN 273
Cdd:COG2107  233 KFIGMYVNEYTVDLGEeGRRAVRTLLERAYEKGLIPKPK 271
VitK2_biosynth pfam02621
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
1-265 4.63e-74

Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base.


Pssm-ID: 426881  Cd Length: 252  Bit Score: 227.05  E-value: 4.63e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973    1 MKIVFSPCPNDTFIFHAWVHglvPGAPELDVALADIDVTNKLAAgpNGP-DIIKISFAALPWVLSKYALLP--CGGALGR 77
Cdd:pfam02621   1 LRVGHSPYPNDLPLFYALVH---DEGLDFEIVLGDPETLNRMLL--EGElDVSAISSAAYARNADDYVLLPdlSGSALGR 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   78 GCGPLvLVANKPcgiinPADLAGRRVAVPAERSTAYLLFRLWLDQHvpGGVGEIIILPfHEIMPAVRDGLvDAGLVIHES 157
Cdd:pfam02621  76 VYSPL-LVSRVP-----ELDGDGKRVALPGESTTSVLLLRLLLPER--YGKPRYVPMP-DEIMAAVLEGE-DAGLLIGDS 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  158 RFTYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLDLS---AITGWLRESVKYAWAHPEASQEYVLRHAQELspeva 234
Cdd:pfam02621 146 ALTYAERGLKKVLDLGEWWKELTGLPMPFGLWVVRRDLALEtakELEEALRASKEYALAHPDEIAEYAAEHAQEM----- 220
                         250       260       270
                  ....*....|....*....|....*....|..
gi 257780973  235 KAHIRLYVNEFTLNLGE-GYGAVISLLSRAAQ 265
Cdd:pfam02621 221 EEFLRLYVNELSYDLGEeGRAGLEEFYERAAE 252
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
83-276 1.68e-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: 45.43  E-value: 1.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   83 VLVANKPCGIINPADLAGRRVAVPaERSTAYLLFRLWLDQH-VPGGVGEIIILPFHEIMPAVRDGLVDAGLVihesrftY 161
Cdd:TIGR01728  84 AIVVIKGSPIRTVADLKGKRIAVP-KGGSGHDLLLRALLKAgLSGDDVTILYLGPSDARAAFAAGQVDAWAI-------W 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  162 PSFGLTLLVDLGSW----WEsDTNLPIPLGAIVARRTL------DLSAITGWLRESVKYAWAHPEASQEYVLRHAQELSP 231
Cdd:TIGR01728 156 EPWGSALVEEGGARvlanGE-GIGLPGQPGFLVVRREFaeahpeQVQRVLKVLVKARKWAEENPEESAKILAKELGLSQA 234
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 257780973  232 EVAK--AHIRLYVNEFTLNLgegygAVISLLSRA---AQAGLIP-DVNLSK 276
Cdd:TIGR01728 235 VVEEtvLNRRFLRVEVISDA-----VVDALQAMAdffYAAGLLKkKPDLKD 280
 
Name Accession Description Interval E-value
PBP2_Ttha1568_Mqnd cd13635
A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This ...
1-264 5.58e-127

A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold; This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ttha1568 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. 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.


Pssm-ID: 270353  Cd Length: 260  Bit Score: 361.45  E-value: 5.58e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   1 MKIVFSPCPNDTFIFHAWVHGLVPGAP-ELDVALADIDVTNKLAAGpNGPDIIKISFAALPWVLSKYALLPCGGALGRGC 79
Cdd:cd13635    2 LSLGISPCPNDTFIFGALLHGLIDTPGlTFDVFLADVETLNRLALE-GRLDVTKLSFAALPHLLDDYALLRSGGALGRGC 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVlVANKPCGIinpADLAGRRVAVPAERSTAYLLFRLWLdqhvpGGVGEIIILPFHEIMPAVRDGLVDAGLVIHESRF 159
Cdd:cd13635   81 GPLL-VARKPDSI---EDLRGKRIAIPGENTTAHLLLRLFY-----PDDFELVPMRFDEIMPAVLRGEVDAGVIIHEGRF 151
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 160 TYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLD---LSAITGWLRESVKYAWAHPEASQEYVLRHAQELSPEVAKA 236
Cdd:cd13635  152 TYQDYGLHKLLDLGEWWEEETGLPIPLGGIVIRRDLGaalARAIEEAIRRSLEYARAHPEAARPYIREHAQELDDEVIRQ 231
                        250       260
                 ....*....|....*....|....*....
gi 257780973 237 HIRLYVNEFTLNLG-EGYGAVISLLSRAA 264
Cdd:cd13635  232 HIDLYVNEFSLDLGeEGRAAVATLLERAE 260
MqnD COG2107
1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme ...
1-273 2.15e-124

1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]; 1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis


Pssm-ID: 441710  Cd Length: 276  Bit Score: 355.60  E-value: 2.15e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   1 MKIVFSPCPNDTFIFHAWVHGLVP-GAPELDVALADIDVTNKLAAgpNGP-DIIKISFAALPWVLSKYALLPCGGALGRG 78
Cdd:COG2107    4 ITLGHSPDPDDAFMFYALAHGKVDtEGFEFEHVLEDIETLNRRAL--KGElDVTAISFHAYPYIADDYALLRSGASLGRG 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  79 CGPLVlVANKPcgiINPADLAGRRVAVPAERSTAYLLFRLWLdqhvpGGVGEIIILPFHEIMPAVRDGLVDAGLVIHESR 158
Cdd:COG2107   82 YGPLV-VAKKP---MSLEELKGKRIAVPGRYTTAYLLLRLAL-----PKAFEVVEMPFDEIMPAVLSGEVDAGLIIHEGQ 152
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 159 FTYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLDLSAITGW---LRESVKYAWAHPEASQEYVLRHAQELSPEVAK 235
Cdd:COG2107  153 LTYAEYGLVKVLDLGEWWEEETGLPLPLGGNVIRRDLGEEVARKIeeaLRKSIKYALAHPDEALEYAMKYARELDEEVID 232
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 257780973 236 AHIRLYVNEFTLNLGE-GYGAVISLLSRAAQAGLIPDVN 273
Cdd:COG2107  233 KFIGMYVNEYTVDLGEeGRRAVRTLLERAYEKGLIPKPK 271
PBP2_Af1704 cd13636
The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold; ...
6-263 1.89e-74

The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold; This group includes the Af1704 protein from from Archaeoglobus fulgidus DSM 4304, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Af1704 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. 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.


Pssm-ID: 270354  Cd Length: 259  Bit Score: 228.26  E-value: 1.89e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   6 SPCPNDTFIFHAWVHGLVPGAP-ELDVALADIDVTNKLAAgpNGP-DIIKISFAALPWVLSKYALLPCGGALGRGCGPLV 83
Cdd:cd13636    7 SPDPDDAFMFYALATGKIDTPGfEFEHVLEDIETLNREAL--EGElDVTAISAHAYAYVADKYALLSSGASMGDGYGPMV 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  84 lVANKPCGiinPADLAGRRVAVPAERSTAYLLFRLWLDQHvpggvgEIIILPFHEIMPAVRDGLVDAGLVIHESRFTYPS 163
Cdd:cd13636   85 -VAKEELT---PEELKGKRIAVPGTLTTAYLLLRLYLPKF------EVVVVPFDEIPDAVLSGEVDAGLIIHEGQLTYER 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 164 FGLTLLVDLGSWWESDTNLPIPLGAIVARRTLD---LSAITGWLRESVKYAWAHPEASQEYVLRHAQELSPEVAKAHIRL 240
Cdd:cd13636  155 EGLKKVVDLGEWWKERTGLPLPLGGNVIRKDLGeevIREIARLLRESIQYALAHREEALEYAMQFARGLDRELADRFVGM 234
                        250       260
                 ....*....|....*....|....
gi 257780973 241 YVNEFTLNLGE-GYGAVISLLSRA 263
Cdd:cd13636  235 YVNDYTLDYGEeGREAVRLLLEMA 258
VitK2_biosynth pfam02621
Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone ...
1-265 4.63e-74

Menaquinone biosynthesis; This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base.


Pssm-ID: 426881  Cd Length: 252  Bit Score: 227.05  E-value: 4.63e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973    1 MKIVFSPCPNDTFIFHAWVHglvPGAPELDVALADIDVTNKLAAgpNGP-DIIKISFAALPWVLSKYALLP--CGGALGR 77
Cdd:pfam02621   1 LRVGHSPYPNDLPLFYALVH---DEGLDFEIVLGDPETLNRMLL--EGElDVSAISSAAYARNADDYVLLPdlSGSALGR 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   78 GCGPLvLVANKPcgiinPADLAGRRVAVPAERSTAYLLFRLWLDQHvpGGVGEIIILPfHEIMPAVRDGLvDAGLVIHES 157
Cdd:pfam02621  76 VYSPL-LVSRVP-----ELDGDGKRVALPGESTTSVLLLRLLLPER--YGKPRYVPMP-DEIMAAVLEGE-DAGLLIGDS 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  158 RFTYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTLDLS---AITGWLRESVKYAWAHPEASQEYVLRHAQELspeva 234
Cdd:pfam02621 146 ALTYAERGLKKVLDLGEWWKELTGLPMPFGLWVVRRDLALEtakELEEALRASKEYALAHPDEIAEYAAEHAQEM----- 220
                         250       260       270
                  ....*....|....*....|....*....|..
gi 257780973  235 KAHIRLYVNEFTLNLGE-GYGAVISLLSRAAQ 265
Cdd:pfam02621 221 EEFLRLYVNELSYDLGEeGRAGLEEFYERAAE 252
PBP2_MqnD_like cd13534
Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 ...
2-251 7.58e-52

Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 periplasmic-binding protein fold; This family represents MqnD, an enzyme within the alternative menaquinone biosynthetic pathway, and related conserved hypothetical proteins. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. The members include Ttha1568, MqnD from Thermus thermophiles HB8, and the conserved hypothetical proteins SCO4506 from Streptomyces coelicolor, Af1704 from Archaeoglobus DSM 4304, Dr0370 from Deinococcus radiodurans, and Ca3427 from candida albicans. They all have significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily (PBP2). 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.


Pssm-ID: 270252 [Multi-domain]  Cd Length: 261  Bit Score: 170.29  E-value: 7.58e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   2 KIVFSPCPNDTFIFHAWVHGLVPGAP-ELDVALADIDVTNKLAAgPNGPDIIKISFAALPWVLSKYALLPCGGALGRGCG 80
Cdd:cd13534    3 RVGHSPDADDLFLFYALKHGWVKETDlIFENVKEDVETLNELAL-KNELDVSAISFAAYPKIADDYVILPTGAVFGDGYG 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  81 PlVLVANKPCgiinpADLAGRRVAVPAERSTAYLLFRLWLDQHvpggvGEIIILPFHEIMPAVRDGLVDAGLVIHESRF- 159
Cdd:cd13534   82 P-VLVAKSPL-----DDKQGKRVAVSGRNTTAYLLLKLLAPQY-----FRPIVVRFDDIEDAVLEGEVDAGVLIHESILm 150
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 160 TYPSFGLTLLVDLGSWWESDTNLPIPLGAIVARRTL--DLS-AITGWLRESVKYAWAHPEASQEYVLRHAQE--LSPEVA 234
Cdd:cd13534  151 TYPRYGLKVVRDLWDLWKESTNLPLPLGVVAIRRDLgeDLIrAFKEAVLLSKAYALAHPDEAIEYMLQEAREirLDEEVL 230
                        250
                 ....*....|....*..
gi 257780973 235 KAHIRLYVNEFTLNLGE 251
Cdd:cd13534  231 KKYLKTYVNEYSNRTGE 247
TauA COG0715
ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion ...
80-271 1.66e-09

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


Pssm-ID: 440479 [Multi-domain]  Cd Length: 297  Bit Score: 57.32  E-value: 1.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVLVANKPCGIINPADLAGRRVAVPAErSTAYLLFRLWLDQH--VPGGVgEIIILPFHEIMPAVRDGLVDAGlvihes 157
Cdd:COG0715  103 GGNALVVRKDSGIKSLADLKGKKVAVPGG-STSHYLLRALLAKAglDPKDV-EIVNLPPPDAVAALLAGQVDAA------ 174
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 158 rFTYPSFgLTLLVDLGSW----WESDTNLPIPLGAIVARRTL------DLSAITGWLRESVKYAWAHPEASQEYVLRHAQ 227
Cdd:COG0715  175 -VVWEPF-ESQAEKKGGGrvlaDSADLVPGYPGDVLVASEDFleenpeAVKAFLRALLKAWAWAAANPDEAAAILAKATG 252
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 257780973 228 eLSPEVAKAHIRLYVNEFTLNLGEGYGAVISLLSRAAQAGLIPD 271
Cdd:COG0715  253 -LDPEVLAAALEGDLRLDPPLGAPDPARLQRVADFLVELGLLPK 295
PhnD COG3221
ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion ...
83-196 1.67e-07

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


Pssm-ID: 442454 [Multi-domain]  Cd Length: 250  Bit Score: 51.08  E-value: 1.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  83 VLVANKPCGIINPADLAGRRVAVPAERSTA-YLLFRLWLDQH--VPGG-VGEIIILPFHE--IMpAVRDGLVDAGLVIHE 156
Cdd:COG3221   85 VIIVRADSPIKSLEDLKGKRFAFGDPDSTSgYLVPRALLAEAglDPERdFSEVVFSGSHDavIL-AVANGQADAGAVDSG 163
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 257780973 157 SRFTYPSFGLTlLVDLGSWWESDtnlPIPLGAIVARRTLD 196
Cdd:COG3221  164 VLERLVEEGPD-ADQLRVIWESP---PIPNDPFVARPDLP 199
PBP2_NrtA_CpmA_like cd13553
Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 ...
83-153 3.26e-07

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: 49.88  E-value: 3.26e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 257780973  83 VLVANKPCGIINPADLAGRRVAVPAERSTAYLLFRLWLDQHV--PGGVGEIIILPFHEIMPAVRDGLVDAGLV 153
Cdd:cd13553   84 AIVVSKDSGIKSVADLKGKTIAVPFPGSTHDVLLRYWLAAAGldPGKDVEIVVLPPPDMVAALAAGQIDAYCV 156
PBP2_PhnD_like cd01071
Substrate binding domain of phosphonate uptake system-like, a member of the type 2 ...
83-196 3.36e-06

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: 47.26  E-value: 3.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  83 VLVANKPCGIINPADLAGRRVAVPAERSTA-YLLFRLWLDQHVPGGVGEIIILPF---HE--IMpAVRDGLVDAGLVIHE 156
Cdd:cd01071   94 VIIVRKDSPIKSLEDLKGKTVAFVDPSSTSgYLFPRAMLKDAGIDPPDFFFEVVFagsHDsaLL-AVANGDVDAAATYDS 172
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 257780973 157 SRFTYPSFGLTLLVDLGSWWESDtnlPIPLGAIVARRTLD 196
Cdd:cd01071  173 TLERAAAAGPIDPDDLRVIWRSP---PIPNDPLVVRKDLP 209
PBP2_ThiY_THI5_like_1 cd13652
Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 ...
72-154 1.21e-05

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: 45.07  E-value: 1.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  72 GGALGRGCGPLVLVANKPCGIINPADLAGRRVAVPAERSTAYLLFRLWLDQHvpgGVG----EIIILPFHEIMPAVRDGL 147
Cdd:cd13652   80 GLGTTPGYGPFAIVVRADSGITSPADLVGKKIAVSTLTNILEYTTNAYLKKN---GLDpdkvEFVEVAFPQMVPALENGN 156

                 ....*..
gi 257780973 148 VDAGLVI 154
Cdd:cd13652  157 VDAAVLA 163
PBP2_TAXI_TRAP cd13520
Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic ...
84-150 1.27e-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: 45.69  E-value: 1.27e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 257780973  84 LVANKPCGIINPADLAGRRVAVPAERSTAYLLFRLWLDQH-VPGGVGEIIILPFHEIMPAVRDGLVDA 150
Cdd:cd13520   94 LVVRKDSGIKSIADLKGKRVAVGPPGSGTELTARRLLEAYgLTDDDVKAEYLGLSDAADALKDGQIDA 161
PBP2_NrtA_SsuA_CpmA_like cd01008
Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of ...
73-222 1.41e-05

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: 44.97  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  73 GALGRGCGPLVLVANKPCGIINPADLAGRRVAVPAErSTAYLLFRLWLDQHvpgGVG----EIIILPFHEIMPAVRDGLV 148
Cdd:cd01008   77 AALSRSPNGNGIVVRKDSGITSLADLKGKKIAVTKG-TTGHFLLLKALAKA---GLSvddvELVNLGPADAAAALASGDV 152
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973 149 DAGLVihesrfTYPSFGLT-------LLVDLGSWWESDTnlpiplGAIVARRtldlsaitgwlresvKYAWAHPEASQEY 221
Cdd:cd01008  153 DAWVT------WEPFLSLAekggdarIIVDGGGLPYTDP------SVLVARR---------------DFVEENPEAVKAL 205

                 .
gi 257780973 222 V 222
Cdd:cd01008  206 L 206
SsuA_fam TIGR01728
ABC transporter, substrate-binding protein, aliphatic sulfonates family; Members of this ...
83-276 1.68e-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: 45.43  E-value: 1.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   83 VLVANKPCGIINPADLAGRRVAVPaERSTAYLLFRLWLDQH-VPGGVGEIIILPFHEIMPAVRDGLVDAGLVihesrftY 161
Cdd:TIGR01728  84 AIVVIKGSPIRTVADLKGKRIAVP-KGGSGHDLLLRALLKAgLSGDDVTILYLGPSDARAAFAAGQVDAWAI-------W 155
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  162 PSFGLTLLVDLGSW----WEsDTNLPIPLGAIVARRTL------DLSAITGWLRESVKYAWAHPEASQEYVLRHAQELSP 231
Cdd:TIGR01728 156 EPWGSALVEEGGARvlanGE-GIGLPGQPGFLVVRREFaeahpeQVQRVLKVLVKARKWAEENPEESAKILAKELGLSQA 234
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 257780973  232 EVAK--AHIRLYVNEFTLNLgegygAVISLLSRA---AQAGLIP-DVNLSK 276
Cdd:TIGR01728 235 VVEEtvLNRRFLRVEVISDA-----VVDALQAMAdffYAAGLLKkKPDLKD 280
PBP2_taurine cd13560
Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold; This ...
84-150 4.42e-05

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: 43.45  E-value: 4.42e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 257780973  84 LVANKPCGIINPADLAGRRVAVPAERSTAYLLFRLWLDQHVPGGVGEIIILPFHEIMPAVRDGLVDA 150
Cdd:cd13560   85 LVVRKGSGIKSLKDLAGKKVAVPFGSTAHYSLLAALKHAGVDPGKVKILDMQPPEIVAAWQRGDIDA 151
PBP2_TRAP_BpDctp6_7 cd13602
Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ...
80-232 1.58e-04

Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold; DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). 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.


Pssm-ID: 270320 [Multi-domain]  Cd Length: 300  Bit Score: 42.21  E-value: 1.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVLVANKPcgIINPADLAGRRVAVPaERSTAyLLFRLWldqhvpGGVGeiIILPFHEIMPAVRDGLVDAGLvihesrf 159
Cdd:cd13602  120 PPQGLFSKKP--ITSLADLKGLKIRTY-DPTTA-EFVEAL------GAAP--VTLPFAEVVPALATGVIDCAL------- 180
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 257780973 160 TYPSFGLTllvdlGSWWE-----SDTNLPIPLGAIVARRTldlsaitgwlresvkyAW-AHPEASQEYVLRHAQELSPE 232
Cdd:cd13602  181 TSTSSGVD-----GKWWEvtkhfYPINYGWPLNMVAVNLD----------------AWnALSPDVQAALLEAAAELEDE 238
Phosphonate-bd pfam12974
ABC transporter, phosphonate, periplasmic substrate-binding protein; This is a family of ...
83-196 2.09e-04

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: 41.87  E-value: 2.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973   83 VLVANKPCGIINPADLAGRRVAVPAERST-AYLLFRLWLDQH---VPGGVGEIIILPFHE-IMPAVRDGLVDAGLVIHES 157
Cdd:pfam12974  88 VIIVRKDSPIQSLEDLKGKTVAFGDPSSTsGYLVPLALLFAEaglDPEDDFKPVFSGSHDaVALAVLNGDADAGAVNSEV 167
                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 257780973  158 RFTYPSFGLTLLVDLGSWWESDtnlPIPLGAIVARRTLD 196
Cdd:pfam12974 168 LERLVAEGPIDRDQLRVIAESP---PIPNDPLVARPDLP 203
Imp COG2358
TRAP-type uncharacterized transport system, periplasmic component [General function prediction ...
81-154 2.28e-04

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


Pssm-ID: 441925 [Multi-domain]  Cd Length: 303  Bit Score: 41.75  E-value: 2.28e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 257780973  81 PLVLVANKPCGIINPADLAGRRVAVPAERSTAYLLFRLWLDQHvpgGVG----EIIILPFHEIMPAVRDGLVDAGLVI 154
Cdd:COG2358  103 PVHLVVRADSGIKSLADLKGKRVSVGPPGSGTEVTAERLLEAA---GLTyddvKVEYLGYGEAADALKDGQIDAAFFV 177
PBP2_BvgS_HisK_like cd01007
The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine ...
81-150 5.26e-03

The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins; This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor 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: 270228 [Multi-domain]  Cd Length: 220  Bit Score: 37.51  E-value: 5.26e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 257780973  81 PLVLVANKPCGII-NPADLAGRRVAVPaeRSTAYLlfrLWLDQHVPggvgEIIILPF---HEIMPAVRDGLVDA 150
Cdd:cd01007   89 PLVIVTRKDAPFInSLSDLAGKRVAVV--KGYALE---ELLRERYP----NINLVEVdstEEALEAVASGEADA 153
Periplasmic_Binding_Protein_Type_2 cd00648
Type 2 periplasmic binding fold superfamily; This evolutionary model and hierarchy represent ...
80-169 5.90e-03

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: 37.17  E-value: 5.90e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 257780973  80 GPLVLVANKPCGIINP---ADLAGRRVAVPAERSTAYLLFRLWLDQHVPGGVGEIII-LPFHEIMPA-VRDGLVDAGLVI 154
Cdd:cd00648   83 GGYVLVVRKGSSIKGLlavADLDGKRVGVGDPGSTAVRQARLALGAYGLKKKDPEVVpVPGTSGALAaVANGAVDAAIVW 162
                         90
                 ....*....|....*..
gi 257780973 155 HES--RFTYPSFGLTLL 169
Cdd:cd00648  163 VPAaeRAQLGNVQLEVL 179
 
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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