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Conserved domains on  [gi|1174722962|ref|WP_081496554|]
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MULTISPECIES: AraC family transcriptional regulator [Marinobacter]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 14401298)

AraC family transcriptional regulator containing a cupin domain as its effector domain and an AraC family helix-turn-helix (HTH) DNA binding domain, controls the expression of genes with diverse biological functions including metabolism, stress response, and virulence

CATH:  2.60.120.10
Gene Ontology:  GO:0003700|GO:0006355|GO:0043565
PubMed:  11282467|33837749|9409145|12270809|19478949|14697267|9573603
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GlxA super family cl34854
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 172-305 5.11e-29

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


The actual alignment was detected with superfamily member COG4977:

Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 112.94  E-value: 5.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 172 ARGLIHASNRLRQllAAVPINADETSQARQAELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHF 251
Cdd:COG4977   182 ARRLVVDPRRPGG--QAQFSPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYL 259

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1174722962 252 LHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRHTAR 305
Cdd:COG4977   260 QRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFR 313
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 46-128 8.22e-25

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


:

Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 95.24  E-value: 8.22e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  46 LTRELYPLAFGHYRRAAGHHMH---REHHrdnLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIH 122
Cdd:cd06986     1 ISSDLYLTDCGYEPCEPGHSYGpavRDYY---ILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDPWTYY 77


                  ....*.
gi 1174722962 123 WVHYTG 128
Cdd:cd06986    78 WIGFSG 83
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 172-305 5.11e-29

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 112.94  E-value: 5.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 172 ARGLIHASNRLRQllAAVPINADETSQARQAELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHF 251
Cdd:COG4977   182 ARRLVVDPRRPGG--QAQFSPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYL 259

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1174722962 252 LHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRHTAR 305
Cdd:COG4977   260 QRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFR 313
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
94-301 4.84e-26

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 104.29  E-value: 4.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  94 TVEAGDLLLLPAGASHRYTADPDNP-WTIHWVhYTGPLA--EDFGQYmgfddSTRIRHLGR----QPRLLVDFNGLLS-V 165
Cdd:PRK10572   70 VCRPGDLLLFPPGEIHHYGRHPDSDeWYHQWV-YFRPRAywADWLNW-----PSIFAGVGRlripDEALQPEFSDLFGqI 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 166 RQTGfrargliHASNRLRQLLAavpINADETSQARQAELDSLHS-------------FMREHLEERLTLNQLAELSGLSP 232
Cdd:PRK10572  144 EQAG-------QSEGRYSELLA---MNLLERLLLRCMEAIPESLhppmdprvreacqYISDHLASEFDIESVAQHVCLSP 213

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962 233 AHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYR 301
Cdd:PRK10572  214 SRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 46-128 8.22e-25

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 95.24  E-value: 8.22e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  46 LTRELYPLAFGHYRRAAGHHMH---REHHrdnLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIH 122
Cdd:cd06986     1 ISSDLYLTDCGYEPCEPGHSYGpavRDYY---ILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDPWTYY 77


                  ....*.
gi 1174722962 123 WVHYTG 128
Cdd:cd06986    78 WIGFSG 83
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
218-301 9.43e-24

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 92.23  E-value: 9.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  218 RLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSP 297
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1174722962  298 TDYR 301
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
224-301 1.92e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 75.32  E-value: 1.92e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962 224 LAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELL-DTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYR 301
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 55-134 2.09e-11

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 60.53  E-value: 2.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  55 FGHYRRAAGHHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHYTGPLAEDF 134
Cdd:pfam02311   5 EGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERI 84
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
53-126 4.29e-09

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.93  E-value: 4.29e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174722962  53 LAFGHYRRAAGHHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHY 126
Cdd:COG1917    23 LEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFS 96
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 214-301 6.56e-08

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 53.14  E-value: 6.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 214 HLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTtSQSFADISRQLGYDDAYYFSRLFKKVM 293
Cdd:TIGR04094 297 NLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHT 375


                  ....*...
gi 1174722962 294 GKSPTDYR 301
Cdd:TIGR04094 376 GVSPKQYQ 383
PRK11171 PRK11171
(S)-ureidoglycine aminohydrolase;
76-125 1.01e-03

(S)-ureidoglycine aminohydrolase;


Pssm-ID: 183011 [Multi-domain]  Cd Length: 266  Bit Score: 39.88  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1174722962  76 LIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVH 125
Cdd:PRK11171   86 FLFVVEGEITLTLEGKTHALSEGGYAYLPPGSDWTLRNAGAEDARFHWIR 135
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 172-305 5.11e-29

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 112.94  E-value: 5.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 172 ARGLIHASNRLRQllAAVPINADETSQARQAELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHF 251
Cdd:COG4977   182 ARRLVVDPRRPGG--QAQFSPLLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYL 259

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1174722962 252 LHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRHTAR 305
Cdd:COG4977   260 QRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFR 313
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
94-301 4.84e-26

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 104.29  E-value: 4.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  94 TVEAGDLLLLPAGASHRYTADPDNP-WTIHWVhYTGPLA--EDFGQYmgfddSTRIRHLGR----QPRLLVDFNGLLS-V 165
Cdd:PRK10572   70 VCRPGDLLLFPPGEIHHYGRHPDSDeWYHQWV-YFRPRAywADWLNW-----PSIFAGVGRlripDEALQPEFSDLFGqI 143

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 166 RQTGfrargliHASNRLRQLLAavpINADETSQARQAELDSLHS-------------FMREHLEERLTLNQLAELSGLSP 232
Cdd:PRK10572  144 EQAG-------QSEGRYSELLA---MNLLERLLLRCMEAIPESLhppmdprvreacqYISDHLASEFDIESVAQHVCLSP 213

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962 233 AHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYR 301
Cdd:PRK10572  214 SRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFR 282
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 46-128 8.22e-25

AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site.


Pssm-ID: 380391 [Multi-domain]  Cd Length: 84  Bit Score: 95.24  E-value: 8.22e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  46 LTRELYPLAFGHYRRAAGHHMH---REHHrdnLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIH 122
Cdd:cd06986     1 ISSDLYLTDCGYEPCEPGHSYGpavRDYY---ILHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPHSYGADEDDPWTYY 77


                  ....*.
gi 1174722962 123 WVHYTG 128
Cdd:cd06986    78 WIGFSG 83
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
218-301 9.43e-24

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 92.23  E-value: 9.43e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  218 RLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSP 297
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1174722962  298 TDYR 301
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
64-306 1.49e-23

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 97.16  E-value: 1.49e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  64 HHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHYTGPLAEDFGQYMGFDDS 143
Cdd:COG2207    14 LALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVG 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 144 TRIRHLGRQPRLLVDFNGLLSVRQTGFRARGLIHASNRLRQLLAAVPINADETSQARQAELDSLHSFMREHLEERLTLNQ 223
Cdd:COG2207    94 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEE 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 224 LAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRHT 303
Cdd:COG2207   174 LARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKR 253


                  ...
gi 1174722962 304 ARH 306
Cdd:COG2207   254 LRA 256
HTH_18 pfam12833
Helix-turn-helix domain;
224-301 1.92e-17

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 75.32  E-value: 1.92e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962 224 LAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELL-DTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYR 301
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79
ftrA PRK09393
transcriptional activator FtrA; Provisional
 197-301 2.48e-14

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 72.30  E-value: 2.48e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 197 SQARQAELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQ 276
Cdd:PRK09393  213 ASRESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAER 292

                          90       100
                  ....*....|....*....|....*
gi 1174722962 277 LGYDDAYYFSRLFKKVMGKSPTDYR 301
Cdd:PRK09393  293 AGFGSEESLRHHFRRRAATSPAAYR 317
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 210-305 6.26e-13

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 68.16  E-value: 6.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 210 FMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDtTSQSFADISRQLGYDDAYYFSRLF 289
Cdd:COG2169    92 LIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFGSLSRFYEAF 170

                          90
                  ....*....|....*.
gi 1174722962 290 KKVMGKSPTDYRHTAR 305
Cdd:COG2169   171 KKLLGMTPSAYRRGGA 186
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
204-304 9.67e-12

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 60.71  E-value: 9.67e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 204 LDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAY 283
Cdd:PRK10219    7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQ 86

                          90       100
                  ....*....|....*....|.
gi 1174722962 284 YFSRLFKKVMGKSPTDYRHTA 304
Cdd:PRK10219   87 TFSRVFRRQFDRTPSDYRHRL 107
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 55-134 2.09e-11

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 60.53  E-value: 2.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  55 FGHYRRAAGHHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHYTGPLAEDF 134
Cdd:pfam02311   5 EGIEARYPGHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDGWRYRWLYFEPELLERI 84
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
53-126 4.29e-09

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.93  E-value: 4.29e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1174722962  53 LAFGHYRRAAGHHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHY 126
Cdd:COG1917    23 LEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVVFS 96
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
175-302 2.93e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 53.95  E-value: 2.93e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 175 LIHASNRLRQLLAAVPINADETSqarqaeLDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHL 254
Cdd:PRK13500  185 LVMLLNRHRYTSDSLPPTSSETL------LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQV 258

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1174722962 255 KVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRH 302
Cdd:PRK13500  259 RVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRH 306
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
175-302 4.18e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 53.52  E-value: 4.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 175 LIHASNRLRQLLAAVPINADETSqarqaeLDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHL 254
Cdd:PRK13502  155 LVMTLKRHRYATDDLPATSRETL------LDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQV 228

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1174722962 255 KVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRH 302
Cdd:PRK13502  229 RICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWRH 276
adjacent_YSIRK TIGR04094
YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only ...
 214-301 6.56e-08

YSIRK-targeted surface antigen transcriptional regulator; Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain.


Pssm-ID: 274977 [Multi-domain]  Cd Length: 383  Bit Score: 53.14  E-value: 6.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 214 HLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTtSQSFADISRQLGYDDAYYFSRLFKKVM 293
Cdd:TIGR04094 297 NLYDPLKVEEIAKQFFMSESKLRKLFKKEMGISIQEYISKRKIEEAKYLLRS-QIPVSEVSNELGFYDLSHFSRTFKKHT 375


                  ....*...
gi 1174722962 294 GKSPTDYR 301
Cdd:TIGR04094 376 GVSPKQYQ 383
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
203-306 7.94e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 52.60  E-value: 7.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 203 ELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDA 282
Cdd:PRK13501  177 QLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDS 256

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1174722962 283 YYFSRLFKKVMGKSPTDYR--------HTARH 306
Cdd:PRK13501  257 NYFSAVFTREAGMTPRDYRqrfirspvLPAKN 288
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 265-302 1.51e-07

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 47.15  E-value: 1.51e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1174722962 265 TTSQSFADISRQLGYDdAYYFSRLFKKVMGKSPTDYRH 302
Cdd:pfam00165   6 STNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYRH 42
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 185-305 2.01e-07

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 51.57  E-value: 2.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 185 LLAAVPINADETSQARQAELDSLHSFMREHL-EERLTLNQLAELSGLSPAHFatrYR--EQTGTSPIQHFLHLKVERACE 261
Cdd:PRK09685  180 LLRPALHQRESVQPRRERQFQKVVALIDQSIqEEILRPEWIAGELGISVRSL---YRlfAEQGLVVAQYIRNRRLDRCAD 256

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1174722962 262 LL--DTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDYRHTAR 305
Cdd:PRK09685  257 DLrpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
65-133 3.92e-07

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 47.83  E-value: 3.92e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962  65 HMHreHHRDNLLiYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVHYTGPLAED 133
Cdd:COG0662    43 HVH--PHRDEFF-YVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELLEVQAPAYLGED 108
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 68-117 9.48e-07

ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized.


Pssm-ID: 281122  Cd Length: 157  Bit Score: 47.74  E-value: 9.48e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1174722962  68 REH-HRDNLLIYCTDGKAFLNVAGVPHT-----VEAGDLLLLPAGASHRYTADPDN 117
Cdd:pfam03079  86 EEHlHTDEEIRYIVEGTGYFDVRDKDDVwirvfVEKGDLISLPAGIYHRFTTTPDN 141
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 211-250 9.50e-07

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 44.84  E-value: 9.50e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1174722962 211 MREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQH 250
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQY 40
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
202-302 1.20e-06

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 48.90  E-value: 1.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 202 AELDSLHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDD 281
Cdd:PRK13503  171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGD 250

                          90       100
                  ....*....|....*....|.
gi 1174722962 282 AYYFSRLFKKVMGKSPTDYRH 302
Cdd:PRK13503  251 SNHFSTLFRREFSWSPRDIRQ 271
cupin_HP0902-like cd02230
Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes ...
 76-113 3.49e-06

Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity.


Pssm-ID: 380358 [Multi-domain]  Cd Length: 83  Bit Score: 44.42  E-value: 3.49e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1174722962  76 LIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTA 113
Cdd:cd02230    34 TVQVLEGEAEFTIGGETVTLKAGELIVMPANVPHALKA 71
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 66-125 7.42e-06

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 43.02  E-value: 7.42e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  66 MHReHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVH 125
Cdd:pfam07883  13 PHR-HPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLDVY 71
PRK10371 PRK10371
transcriptional regulator MelR;
209-305 1.07e-05

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 46.35  E-value: 1.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 209 SFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRL 288
Cdd:PRK10371  198 GFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYST 277

                          90
                  ....*....|....*..
gi 1174722962 289 FKKVMGKSPTDYRHTAR 305
Cdd:PRK10371  278 FGKYVGMSPQQYRKLSQ 294
cupin_UGlyAH_N cd02211
(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family ...
 76-124 1.17e-05

(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved "jelly roll-like" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features.


Pssm-ID: 380341 [Multi-domain]  Cd Length: 117  Bit Score: 43.66  E-value: 1.17e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1174722962  76 LIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWV 124
Cdd:cd02211    50 FLYVLEGEVELTVGGETHTLTAGGYAYLPPGTKHSLRNAGDEPARLLWY 98
cupin_TcmJ-like cd06991
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ...
 55-131 1.45e-05

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380396 [Multi-domain]  Cd Length: 105  Bit Score: 43.05  E-value: 1.45e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1174722962  55 FGHYRRAAGHHMhREHHRD--NLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIhwVHYTGPLA 131
Cdd:cd06991    21 MGTLTLAPGERV-SEHYHPysEEFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDEPARL--VFHLSPLA 96
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 55-125 2.93e-05

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 41.31  E-value: 2.93e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1174722962  55 FGHYRRAAGHHMHREHHRDNL-LIYCTDGKAFLNV-AGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVH 125
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPEQDeIFYVLSGEGELTLdDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVVS 73
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 52-123 3.13e-05

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 41.45  E-value: 3.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1174722962  52 PLAFGHYRRAAGHHMHREHHRDNLLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNP---WTIHW 123
Cdd:cd06988     1 PFGGAWCVVRPGTTSTPHSHHEYEIFIVISGKGIVVVDGEREPVKAGDVVYIPPGTEHYVKNDGDEDfefYSIWW 75
AllE COG3257
Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];
77-125 1.32e-04

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];


Pssm-ID: 442488 [Multi-domain]  Cd Length: 262  Bit Score: 42.50  E-value: 1.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1174722962  77 IYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVH 125
Cdd:COG3257    85 LFVLEGEVTLTLGGETHELTPGGYAYLPPGTPWTLRNAGDEPARFHWIR 133
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 64-119 7.22e-04

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 37.81  E-value: 7.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1174722962  64 HHMHREHHrdnlLIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPW 119
Cdd:cd02222    32 LHTHPWEH----EVYVLRGKGVVVIGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPL 83
PRK11171 PRK11171
(S)-ureidoglycine aminohydrolase;
76-125 1.01e-03

(S)-ureidoglycine aminohydrolase;


Pssm-ID: 183011 [Multi-domain]  Cd Length: 266  Bit Score: 39.88  E-value: 1.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1174722962  76 LIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYTADPDNPWTIHWVH 125
Cdd:PRK11171   86 FLFVVEGEITLTLEGKTHALSEGGYAYLPPGSDWTLRNAGAEDARFHWIR 135
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
24-137 1.25e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 38.07  E-value: 1.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  24 VPADSVRYVVPEPIVRLLA-AHPLTRelypLAFGHYRRAAGH---HMHReHHRDNLLIYCTDGKAFLNVAGVPHTVEAGD 99
Cdd:COG3837     2 VNLDDLPGPEAGRRYRRLGdALGLTR----LGVNLITLPPGAsssPYHA-HSAEEEFVYVLEGELTLRIGGEEYVLEPGD 76

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1174722962 100 LLLLPAGASHRYTADPDNPWTIHWVHYTGPLAEDFGQY 137
Cdd:COG3837    77 SVGFPAGVPHRLRNRGDEPARYLVVGTRAPYPDSFDYW 114
cupin_QDO_N_C cd02215
quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known ...
 65-139 1.38e-03

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.


Pssm-ID: 380345 [Multi-domain]  Cd Length: 122  Bit Score: 37.90  E-value: 1.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1174722962  65 HMHREHHRDnllIYCTDGKAFLNVAGVPHTVEAGDLLLLPAGASHRYT-ADPDNPWtIHWVhyTGPLAEDFGQYMG 139
Cdd:cd02215    48 HYHKRHHET---FYVLEGRLQLWLDGESRLLTPGDFASVPPGTIHAYRmLSPDTRF-LGVI--TPGGFERFFRALG 117
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 221-301 1.76e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 39.36  E-value: 1.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 221 LNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTDY 300
Cdd:PRK10296  191 LENMVRLSGKSQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSY 270


                  .
gi 1174722962 301 R 301
Cdd:PRK10296  271 R 271
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
207-301 2.55e-03

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 38.84  E-value: 2.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 207 LHSFMREHLEERLTLNQLAELSGLSPAHFATRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFS 286
Cdd:PRK15121   10 LLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFT 89

                          90
                  ....*....|....*
gi 1174722962 287 RLFKKVMGKSPTDYR 301
Cdd:PRK15121   90 RAFKKQFAQTPALYR 104
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 195-300 3.00e-03

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 38.51  E-value: 3.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 195 ETSQARQAEldSLHSFMREHLEERLTLNQLAELSGLSPAHFaTRYREQTGTSPIQHFLHLKVERACELLDTTSQSFADIS 274
Cdd:PRK15186  176 ELSQNTLAE--NIYNIIISDISRKWALKDISDSLYMSCSTL-KRKLKQENTSFSEVYLNARMNKATKLLRNSEYNITRVA 252

                          90       100
                  ....*....|....*....|....*.
gi 1174722962 275 RQLGYDDAYYFSRLFKKVMGKSPTDY 300
Cdd:PRK15186  253 YMCGYDSASYFTCVFKKHFKTTPSEF 278
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 94-117 3.34e-03

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization


Pssm-ID: 380360  Cd Length: 134  Bit Score: 37.14  E-value: 3.34e-03
                          10        20
                  ....*....|....*....|....
gi 1174722962  94 TVEAGDLLLLPAGASHRYTADPDN 117
Cdd:cd02232    95 LVEKGDLIVVPAGIYHRFTLDENP 118
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 220-306 6.60e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 37.60  E-value: 6.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962 220 TLNQLAELSGLSPAHFATRYREQtGTSPIQHFLHLKVERACELLDTTSQSFADISRQLGYDDAYYFSRLFKKVMGKSPTD 299
Cdd:PRK09978  160 TLARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTE 238


                  ....*..
gi 1174722962 300 YRHTARH 306
Cdd:PRK09978  239 YQERSAQ 245
Ves COG3758
Various environmental stresses-induced protein Ves (function unknown) [Function unknown];
44-108 7.74e-03

Various environmental stresses-induced protein Ves (function unknown) [Function unknown];


Pssm-ID: 442972 [Multi-domain]  Cd Length: 196  Bit Score: 36.86  E-value: 7.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1174722962  44 HPLTRELYPLAF-GH------------------YRRAAGHH----------MHREHHRDNLLIYCTDGKAFLNVAGVPHT 94
Cdd:COG3758    81 HTLDEPFQPFAFsGDapvsarllggpvrdfnlmTRRGRARArvrvlrlagtLPLHADAGTGLLYVLAGAWTVALGGEAIT 160

                          90
                  ....*....|....
gi 1174722962  95 VEAGDLLLLPAGAS 108
Cdd:COG3758   161 LEAGDTLLLEAPAP 174
 
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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