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Conserved domains on  [gi|489213359|ref|WP_003122092|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Pseudomonas]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 14398448)

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
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 28-121 1.64e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


:

Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 106.89  E-value: 1.64e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  28 VMAKTFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLHTVYARPQSCPPeFP 107
Cdd:cd06124    3 ARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAG-LP 81

                         90
                 ....*....|....
gi 489213359 108 RVPRGVMVSPLLRE 121
Cdd:cd06124   82 AEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
188-265 4.11e-16

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 71.47  E-value: 4.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  188 WARYVGASSRTLARLFLSELGVTFVHWRHQV--RLAAALPRLAAGEAVARIAVDLGYQTPSAFSAMFRRLTGSTPSRYFA 265
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLrlERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 28-121 1.64e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 106.89  E-value: 1.64e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  28 VMAKTFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLHTVYARPQSCPPeFP 107
Cdd:cd06124    3 ARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAG-LP 81

                         90
                 ....*....|....
gi 489213359 108 RVPRGVMVSPLLRE 121
Cdd:cd06124   82 AEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
188-265 4.11e-16

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 71.47  E-value: 4.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  188 WARYVGASSRTLARLFLSELGVTFVHWRHQV--RLAAALPRLAAGEAVARIAVDLGYQTPSAFSAMFRRLTGSTPSRYFA 265
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLrlERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
32-265 8.06e-15

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 72.12  E-value: 8.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  32 TFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLHTVYARPQSCPPEFPRVPR 111
Cdd:COG2207   25 LLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 112 GVMVSPLLRELIVRAAGLPLLYDERGREGRLMAVLLDELEWSREQPLALPDPADRRLGRICQALLenpadprGLEEWARY 191
Cdd:COG2207  105 LLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL-------TLEELARE 177

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489213359 192 VGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGEA-VARIAVDLGYQTPSAFSAMFRRLTGSTPSRYFA 265
Cdd:COG2207  178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLsISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRK 252
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
182-263 5.34e-14

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 65.65  E-value: 5.34e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359   182 PRGLEEWARYVGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGE-AVARIAVDLGYQTPSAFSAMFRRLTGSTP 260
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 489213359   261 SRY 263
Cdd:smart00342  81 SEY 83
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 157-263 2.23e-13

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: 68.65  E-value: 2.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 157 PLALPDPADRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHW---------RHQVrlaaalprL 227
Cdd:COG4977  201 LLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYlqrlrleraRRLL--------E 272

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489213359 228 AAGEAVARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:COG4977  273 TTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAY 308
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
154-263 1.37e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 60.37  E-value: 1.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 154 REQPLALPDPADRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHWRH-QVRLAAALPRLAAGEA 232
Cdd:PRK10572 171 EAIPESLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREdQRISRAKLLLQTTRMP 250

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489213359 233 VARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:PRK10572 251 IATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 36-146 9.14e-05

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: 41.27  E-value: 9.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359   36 GFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGE--VRLHTVYARP----------QSCP 103
Cdd:pfam02311  13 GHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEdgWRYRWLYFEPelleriladiSILA 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 489213359  104 PEFPRVPRGVMVSPLLRELIvRAAGLPLLYDERGREGRLMAVL 146
Cdd:pfam02311  93 GGPLPLLRDPELAALLRALF-RLLEEAGRSDDLLAEALLYQLL 134
 
Name Accession Description Interval E-value
cupin_NimR-like_N cd06124
AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This ...
 28-121 1.64e-29

AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain; This family contains mostly 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 in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380379 [Multi-domain]  Cd Length: 95  Bit Score: 106.89  E-value: 1.64e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  28 VMAKTFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLHTVYARPQSCPPeFP 107
Cdd:cd06124    3 ARAADYPAGHRTPWHSHPWGQLLYASSGVMTVETEDGRWLVPPQRAVWIPAGVEHSVRMLGAVELRSLYIDPEAAAG-LP 81

                         90
                 ....*....|....
gi 489213359 108 RVPRGVMVSPLLRE 121
Cdd:cd06124   82 AEPCVLAVSPLLRE 95
HTH_18 pfam12833
Helix-turn-helix domain;
188-265 4.11e-16

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 71.47  E-value: 4.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  188 WARYVGASSRTLARLFLSELGVTFVHWRHQV--RLAAALPRLAAGEAVARIAVDLGYQTPSAFSAMFRRLTGSTPSRYFA 265
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLrlERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
32-265 8.06e-15

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 72.12  E-value: 8.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359  32 TFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLHTVYARPQSCPPEFPRVPR 111
Cdd:COG2207   25 LLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLL 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 112 GVMVSPLLRELIVRAAGLPLLYDERGREGRLMAVLLDELEWSREQPLALPDPADRRLGRICQALLenpadprGLEEWARY 191
Cdd:COG2207  105 LLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL-------TLEELARE 177

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489213359 192 VGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGEA-VARIAVDLGYQTPSAFSAMFRRLTGSTPSRYFA 265
Cdd:COG2207  178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLsISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRK 252
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
182-263 5.34e-14

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 65.65  E-value: 5.34e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359   182 PRGLEEWARYVGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGE-AVARIAVDLGYQTPSAFSAMFRRLTGSTP 260
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDlSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 489213359   261 SRY 263
Cdd:smart00342  81 SEY 83
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 157-263 2.23e-13

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: 68.65  E-value: 2.23e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 157 PLALPDPADRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHW---------RHQVrlaaalprL 227
Cdd:COG4977  201 LLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYlqrlrleraRRLL--------E 272

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489213359 228 AAGEAVARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:COG4977  273 TTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAY 308
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 154-263 6.44e-11

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: 61.61  E-value: 6.44e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 154 REQPLALP--DPADRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGE 231
Cdd:COG2169   70 RCRPDLAPgsPPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGL 149

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489213359 232 AVARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:COG2169  150 SVTDAAYAAGFGSLSRFYEAFKKLLGMTPSAY 181
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
154-263 1.37e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 60.37  E-value: 1.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 154 REQPLALPDPADRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHWRH-QVRLAAALPRLAAGEA 232
Cdd:PRK10572 171 EAIPESLHPPMDPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREdQRISRAKLLLQTTRMP 250

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489213359 233 VARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:PRK10572 251 IATIGRNVGYDDQLYFSRVFKKCTGASPSEF 281
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
32-89 9.29e-10

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 54.47  E-value: 9.29e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489213359  32 TFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGE 89
Cdd:COG1917   29 TFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGD 86
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
21-93 7.72e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 41.28  E-value: 7.72e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489213359  21 RVGRPLGVMAKTFPAGFVVAEHRHE-RAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRLH 93
Cdd:COG0662   22 EGGERLSVKRITVPPGAELSLHVHPhRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLE 95
cupin_HP0902-like cd02230
Helicobacter pylori HP0902 and related proteins, cupin domain; This family includes ...
 32-86 7.87e-05

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: 40.19  E-value: 7.87e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489213359  32 TFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLA 86
Cdd:cd02230   17 AFDAGQELSEHTAPGDATVQVLEGEAEFTIGGETVTLKAGELIVMPANVPHALKA 71
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 36-146 9.14e-05

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: 41.27  E-value: 9.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359   36 GFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGE--VRLHTVYARP----------QSCP 103
Cdd:pfam02311  13 GHSFPPHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEdgWRYRWLYFEPelleriladiSILA 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 489213359  104 PEFPRVPRGVMVSPLLRELIvRAAGLPLLYDERGREGRLMAVL 146
Cdd:pfam02311  93 GGPLPLLRDPELAALLRALF-RLLEEAGRSDDLLAEALLYQLL 134
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 32-96 1.78e-04

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: 39.16  E-value: 1.78e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489213359   32 TFPAGFVVAEHRHERA-QLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGE--VRLHTVY 96
Cdd:pfam07883   4 TLPPGESSPPHRHPGEdEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDepARLLDVY 71
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
143-263 4.73e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 40.66  E-value: 4.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 143 MAVLLDELEWSREQPLALPDpaDRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHWRHQVRLAA 222
Cdd:PRK13501 155 LAIVLKRHRYRAEQAHLLPD--GEQLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCH 232

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489213359 223 ALPRLAAGEA-VARIAVDLGYQTPSAFSAMFRRLTGSTPSRY 263
Cdd:PRK13501 233 AKCLLRGSEHrISDIAARCGFEDSNYFSAVFTREAGMTPRDY 274
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 32-96 1.39e-03

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: 36.69  E-value: 1.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489213359  32 TFPAGFVVAEHRHERA-QLIHALSGVIELHV--GRTlWLVPPQRAVWMPAGMAHAMLARGEVRLHTVY 96
Cdd:cd02208    5 TLPPGTSSPPHWHPEQdEIFYVLSGEGELTLddGET-VELKAGDIVLIPPGVPHSFVNTSDEPAVFLV 71
ftrA PRK09393
transcriptional activator FtrA; Provisional
 165-263 1.48e-03

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 39.56  E-value: 1.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 165 DRRLGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHW-RHQVRLAAALPRLAAGEAVARIAVDLGYQ 243
Cdd:PRK09393 217 SDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWlLRERLARARDLLESSALSIDQIAERAGFG 296

                         90       100
                 ....*....|....*....|
gi 489213359 244 TPSAFSAMFRRLTGSTPSRY 263
Cdd:PRK09393 297 SEESLRHHFRRRAATSPAAY 316
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
168-268 2.42e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.50  E-value: 2.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489213359 168 LGRICQALLENPADPRGLEEWARYVGASSRTLARLFLSELGVTFVHWRHQVRLAAALPRLAAGE-AVARIAVDLGYQTPS 246
Cdd:PRK13502 178 LDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPlMISEISMQCGFEDSN 257

                         90       100
                 ....*....|....*....|..
gi 489213359 247 AFSAMFRRLTGSTPSRYFALSD 268
Cdd:PRK13502 258 YFSVVFTRETGMTPSQWRHLSN 279
cupin_DRT102 cd06989
Arabidopsis thaliana DRT102 and related proteins, cupin domain; This family includes bacterial ...
 33-89 2.51e-03

Arabidopsis thaliana DRT102 and related proteins, cupin domain; This family includes bacterial and eukaryotic proteins homologous to DNA-damage-repair/toleration protein DRT102 found in Arabidopsis thaliana. DRT102 may be involved in DNA repair from UV damage. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380394  Cd Length: 97  Bit Score: 36.36  E-value: 2.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489213359  33 FPAGFVVAEHRHERAQLIHALSGVIELHVGRTL------WLvPPQRAVWMPAGMAHAMLARGE 89
Cdd:cd06989   25 FPAGYKIPPHTHPDDERVTVISGTFYLGMGDKFdeakakAL-PAGSFFTLPAGTPHFAWAKDE 86
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 32-92 5.26e-03

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380366 [Multi-domain]  Cd Length: 104  Bit Score: 35.52  E-value: 5.26e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489213359  32 TFPAGFVVAEHRHERAQLIHALSGVIELHVGRTLWLVPPQRAVWMPAGMAHAMLARGEVRL 92
Cdd:cd02238   33 RFEKGAVVPLHSHPHEQIGYVLSGRFEFTIGGETRILKPGDSYYIPPNVPHGAEALEDSVL 93
 
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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