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Conserved domains on  [gi|1737110181|emb|VAE43505|]
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protein YdeC [Enterobacter hormaechei]

Protein Classification

AraC family transcriptional regulator( domain architecture ID 14388536)

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:0043565|GO:0006355
PubMed:  19478949|14697267|9573603|11282467|33837749|9409145|12270809
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
190-273 3.91e-25

helix_turn_helix, arabinose operon control protein;


:

Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 95.31  E-value: 3.91e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  190 KFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETP 269
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1737110181  270 LQYR 273
Cdd:smart00342  81 SEYR 84
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
56-278 7.13e-23

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 94.46  E-value: 7.13e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  56 RHYTMRPGRLFFFPPFTLHKVMVDEQAEAIYRRTIIHLDQHAVLKILRDFPQTRQRLERLSRRGGEAWVADLAHYHHHID 135
Cdd:COG2207    34 LVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 136 HLFSCYKPPMNGESIASLLIGLFAMLPDDRDGEPGNSQGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAET 215
Cdd:COG2207   114 LLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEET 193

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737110181 216 GEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHSS 278
Cdd:COG2207   194 GTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 20-86 2.16e-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: 41.70  E-value: 2.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1737110181  20 ASFSRLFANTVRYHHWHQ-CLEILYVEEGFG-VAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIY 86
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPeQDEIFYVLSGEGeLTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
190-273 3.91e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 95.31  E-value: 3.91e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  190 KFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETP 269
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1737110181  270 LQYR 273
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 160-278 3.10e-23

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: 96.38  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 160 MLPDDRDGepGNSQGIA------------SQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLR 227
Cdd:COG4977   186 VVDPRRPG--GQAQFSPllvplghrdprlARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLR 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1737110181 228 LRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHSS 278
Cdd:COG4977   264 LERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFRA 314
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
56-278 7.13e-23

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 94.46  E-value: 7.13e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  56 RHYTMRPGRLFFFPPFTLHKVMVDEQAEAIYRRTIIHLDQHAVLKILRDFPQTRQRLERLSRRGGEAWVADLAHYHHHID 135
Cdd:COG2207    34 LVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 136 HLFSCYKPPMNGESIASLLIGLFAMLPDDRDGEPGNSQGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAET 215
Cdd:COG2207   114 LLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEET 193

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737110181 216 GEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHSS 278
Cdd:COG2207   194 GTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
HTH_18 pfam12833
Helix-turn-helix domain;
196-275 2.58e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.64  E-value: 2.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 196 LAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLH-TDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRK 274
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1737110181 275 N 275
Cdd:pfam12833  81 R 81
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
34-276 2.80e-13

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 68.16  E-value: 2.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFfppftlhkvmVDEQAEAIYRrtiiHLDQHAVLKILRDFPQTRQRLE 113
Cdd:PRK13503   31 HHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCF----------VRDHDRHLYE----HTDNLCLTNVLYRSPDAFRFLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 114 RLSR-----RGGE---AWVADlAHYHHHIDHLFSCYK---PPMNGESIASLLIGLFAMLPDDRDG----EPGNSQGIASQ 178
Cdd:PRK13503   97 GLNQllpqeQDGQypsHWRVN-QSVLQQVRQLVAQMEqqeESNDLEAIASREILFMQLLVLLRKSslqeNGENSDARLNQ 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 179 VMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFI 258
Cdd:PRK13503  176 LLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFS 255

                         250
                  ....*....|....*...
gi 1737110181 259 SAFKKGIGETPLQYRKNH 276
Cdd:PRK13503  256 TLFRREFSWSPRDIRQGR 273
ftrA PRK09393
transcriptional activator FtrA; Provisional
 161-275 1.54e-11

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 63.44  E-value: 1.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 161 LPDDRDGepGNSQGIA-----------SQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLR 229
Cdd:PRK09393  196 VPPHRDG--GQAQFVPrpvasresdrlGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLA 273

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1737110181 230 KACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKN 275
Cdd:PRK09393  274 RARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAAYRKR 319
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 20-86 2.16e-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: 41.70  E-value: 2.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1737110181  20 ASFSRLFANTVRYHHWHQ-CLEILYVEEGFG-VAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIY 86
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPeQDEIFYVLSGEGeLTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 20-109 5.14e-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: 42.04  E-value: 5.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  20 ASFSRLFANTVRYH---HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEaiYRRTIIHLDQH 96
Cdd:pfam02311   2 PGLEGIEARYPGHSfppHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDG--WRYRWLYFEPE 79

                          90
                  ....*....|...
gi 1737110181  97 AVLKILRDFPQTR 109
Cdd:pfam02311  80 LLERILADISILA 92
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 34-76 7.60e-05

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: 39.93  E-value: 7.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1737110181  34 HWH-QCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKV 76
Cdd:pfam07883  14 HRHpGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRF 57
bicupin_oxalic TIGR03404
bicupin, oxalate decarboxylase family; Members of this protein family are defined as bicupins ...
 24-83 4.52e-03

bicupin, oxalate decarboxylase family; Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.


Pssm-ID: 274565 [Multi-domain]  Cd Length: 367  Bit Score: 38.07  E-value: 4.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737110181  24 RLFANTVRYHHWHQCLEILYVEEG-FGVAIVDN--RHY--TMRPGRLFFFPPFTLHKVM-VDEQAE 83
Cdd:TIGR03404  73 RLEPGAIRELHWHKEAEWAYVLYGsCRITAVDEngRNYidDVGAGDLWYFPPGIPHSLQgLDEGCE 138
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 34-92 6.23e-03

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, 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, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 34.67  E-value: 6.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIYRRTIIH 92
Cdd:cd07001    18 HFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVHSCIQISGRRLDYERINIW 76
 
Name Accession Description Interval E-value
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
190-273 3.91e-25

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 95.31  E-value: 3.91e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  190 KFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETP 269
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1737110181  270 LQYR 273
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 160-278 3.10e-23

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: 96.38  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 160 MLPDDRDGepGNSQGIA------------SQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLR 227
Cdd:COG4977   186 VVDPRRPG--GQAQFSPllvplghrdprlARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLR 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1737110181 228 LRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHSS 278
Cdd:COG4977   264 LERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFRA 314
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
56-278 7.13e-23

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 94.46  E-value: 7.13e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  56 RHYTMRPGRLFFFPPFTLHKVMVDEQAEAIYRRTIIHLDQHAVLKILRDFPQTRQRLERLSRRGGEAWVADLAHYHHHID 135
Cdd:COG2207    34 LVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLL 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 136 HLFSCYKPPMNGESIASLLIGLFAMLPDDRDGEPGNSQGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAET 215
Cdd:COG2207   114 LLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEET 193

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1737110181 216 GEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHSS 278
Cdd:COG2207   194 GTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRA 256
HTH_18 pfam12833
Helix-turn-helix domain;
196-275 2.58e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 82.64  E-value: 2.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 196 LAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLH-TDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRK 274
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1737110181 275 N 275
Cdd:pfam12833  81 R 81
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 162-276 2.65e-20

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: 88.96  E-value: 2.65e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 162 PDDRDGEPGNSQGIAsQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACEcLLHTDSS 241
Cdd:COG2169    73 PDLAPGSPPRADLVA-RACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQ-LLQTGLS 150

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1737110181 242 VRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNH 276
Cdd:COG2169   151 VTDAAYAAGFGSLSRFYEAFKKLLGMTPSAYRRGG 185
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
34-276 2.80e-13

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 68.16  E-value: 2.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFfppftlhkvmVDEQAEAIYRrtiiHLDQHAVLKILRDFPQTRQRLE 113
Cdd:PRK13503   31 HHHDFHEIVIVEHGTGIHVFNGQPYTLSGGTVCF----------VRDHDRHLYE----HTDNLCLTNVLYRSPDAFRFLA 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 114 RLSR-----RGGE---AWVADlAHYHHHIDHLFSCYK---PPMNGESIASLLIGLFAMLPDDRDG----EPGNSQGIASQ 178
Cdd:PRK13503   97 GLNQllpqeQDGQypsHWRVN-QSVLQQVRQLVAQMEqqeESNDLEAIASREILFMQLLVLLRKSslqeNGENSDARLNQ 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 179 VMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFI 258
Cdd:PRK13503  176 LLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFS 255

                         250
                  ....*....|....*...
gi 1737110181 259 SAFKKGIGETPLQYRKNH 276
Cdd:PRK13503  256 TLFRREFSWSPRDIRQGR 273
ftrA PRK09393
transcriptional activator FtrA; Provisional
 161-275 1.54e-11

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 63.44  E-value: 1.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 161 LPDDRDGepGNSQGIA-----------SQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLR 229
Cdd:PRK09393  196 VPPHRDG--GQAQFVPrpvasresdrlGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLA 273

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1737110181 230 KACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKN 275
Cdd:PRK09393  274 RARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSPAAYRKR 319
PRK10371 PRK10371
transcriptional regulator MelR;
154-274 3.43e-11

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 62.53  E-value: 3.43e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 154 LIGLFAMLPDDRDGEPGNS-----QGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRL 228
Cdd:PRK10371  166 LSGWEPILVNKTSRTHKNSvsrhaQFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRI 245

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1737110181 229 RKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRK 274
Cdd:PRK10371  246 NHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSPQQYRK 291
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
173-273 4.52e-11

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 58.40  E-value: 4.52e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 173 QGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFS 252
Cdd:PRK10219    4 QKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYV 83

                          90       100
                  ....*....|....*....|.
gi 1737110181 253 DVTWFISAFKKGIGETPLQYR 273
Cdd:PRK10219   84 SQQTFSRVFRRQFDRTPSDYR 104
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
11-277 1.15e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 60.89  E-value: 1.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  11 ELIALNDTVASFSRLFANTVRYHHWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKV-----MVDEQAEAI 85
Cdd:PRK13500   41 DFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYasvndLVLQNIIYC 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  86 YRRTIIHLD-QHAVLKILRDFPQTRQRLerlsrrgGEAWVADLAHYHHHIDHLFSCYKPPMNgeSIASLLIGLFAMLPDD 164
Cdd:PRK13500  121 PERLKLNLDwQGAIPGFSASAGQPHWRL-------GSVGMAQARQVIGQLEHESSQHVPFAN--EMAELLFGQLVMLLNR 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 165 R-----DGEPGNSQGIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTD 239
Cdd:PRK13500  192 HrytsdSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSR 271

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1737110181 240 SSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHS 277
Cdd:PRK13500  272 LLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNS 309
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
174-275 2.75e-10

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 59.64  E-value: 2.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 174 GIASQVMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSD 253
Cdd:PRK15121    5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFDS 84

                          90       100
                  ....*....|....*....|..
gi 1737110181 254 VTWFISAFKKGIGETPLQYRKN 275
Cdd:PRK15121   85 QQTFTRAFKKQFAQTPALYRRS 106
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
34-273 1.25e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 57.76  E-value: 1.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKV-----MVDEQAEAIYRRTIIHLDQHAVLKilrDFPQT 108
Cdd:PRK13502   34 HTHEFCELVMVWRGNGLHVLNERPYRITRGDLFYIRAEDKHSYtsvndLVLQNIIYCPERLKLNVNWQAMIP---GFQGA 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 109 RQ----RLERLSRRGGEAWVADLAHYHHHIDHLfscykppmnGESIASLLIGLFAM-LPDDR---DGEPGNS-QGIASQV 179
Cdd:PRK13502  111 QWhphwRLGSMGMNQARQVINQLEHESNGRDPL---------ANEMAELLFGQLVMtLKRHRyatDDLPATSrETLLDKL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 180 MFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFIS 259
Cdd:PRK13502  182 ITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSV 261

                         250
                  ....*....|....
gi 1737110181 260 AFKKGIGETPLQYR 273
Cdd:PRK13502  262 VFTRETGMTPSQWR 275
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 139-277 2.49e-09

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 56.96  E-value: 2.49e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 139 SCYKPPMNGESIASLLIGLFAML-P--DDRDGEPGNSQGIASQVMFWLDEHYQ-EKFRLDALAAELGKSRSYVSRRFhAE 214
Cdd:PRK09685  159 SMNGPALSETESEALLEALIALLrPalHQRESVQPRRERQFQKVVALIDQSIQeEILRPEWIAGELGISVRSLYRLF-AE 237

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1737110181 215 TGEKIHDYLNTLRLRKACECL--LHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQYRKNHS 277
Cdd:PRK09685  238 QGLVVAQYIRNRRLDRCADDLrpAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 186-275 2.51e-08

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 53.61  E-value: 2.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 186 HYQEKFRLDALAAEL---GKSRSYVSR---RFHAETGEKIhdyLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFIS 259
Cdd:PRK10296  181 HDKEQFSESALENMVrlsGKSQEYLTRatrRYYGKTPMQI---INEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIK 257

                          90
                  ....*....|....*.
gi 1737110181 260 AFKKGIGETPLQYRKN 275
Cdd:PRK10296  258 TFKKLTSFTPGSYRKK 273
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 183-224 1.49e-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: 46.76  E-value: 1.49e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1737110181 183 LDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLN 224
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
34-86 2.75e-07

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 47.92  E-value: 2.75e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIY 86
Cdd:COG1917    39 HSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVL 91
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
34-274 1.74e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 48.36  E-value: 1.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPF------TLHKVMVDEqaeAIYRRTIIHLDQHAVLKILRDFPQ 107
Cdd:PRK13501   34 HTHQFCEIVIVWRGNGLHVLNDHPYRITCGDVFYIQAAdhhsyeSVHDLVLDN---IIYCPERLHLNAQWHKLLPPLGPE 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 108 TRQRLERLSRRG---GEAWVADLAHYHHHIDhlfscykpPMNGESIASLLIGLFAMLpddrdgepgNSQGIASQVMFWLD 184
Cdd:PRK13501  111 QNQGYWRLTTQGmaqARPIIQQLAQESRKTD--------SWSIQLTEVLLLQLAIVL---------KRHRYRAEQAHLLP 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 185 EHYQEKFRLDALAAELGK-------------SRSYVSRRFHAETGEKIHDYLNTLRLRKAcECLLHT-DSSVRDIAAQAG 250
Cdd:PRK13501  174 DGEQLDLIMSALQQSLGAyfdmadfchknqlVERSLKQLFRQQTGMSISHYLRQIRLCHA-KCLLRGsEHRISDIAARCG 252

                         250       260
                  ....*....|....*....|....
gi 1737110181 251 FSDVTWFISAFKKGIGETPLQYRK 274
Cdd:PRK13501  253 FEDSNYFSAVFTREAGMTPRDYRQ 276
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 236-274 1.37e-05

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: 41.37  E-value: 1.37e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1737110181 236 LHTDSSVRDIAAQAGFSdVTWFISAFKKGIGETPLQYRK 274
Cdd:pfam00165   5 LSTNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYRH 42
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 20-86 2.16e-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: 41.70  E-value: 2.16e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1737110181  20 ASFSRLFANTVRYHHWHQ-CLEILYVEEGFG-VAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIY 86
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPeQDEIFYVLSGEGeLTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 20-109 5.14e-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: 42.04  E-value: 5.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181  20 ASFSRLFANTVRYH---HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEaiYRRTIIHLDQH 96
Cdd:pfam02311   2 PGLEGIEARYPGHSfppHVHDFYVIGYIERGVGRFRLNGRTYHLGPGDLFLLPPGEPHDYEPESEDG--WRYRWLYFEPE 79

                          90
                  ....*....|...
gi 1737110181  97 AVLKILRDFPQTR 109
Cdd:pfam02311  80 LLERILADISILA 92
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
179-273 5.84e-05

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 42.01  E-value: 5.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 179 VMFWLDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFI 258
Cdd:PRK11511   14 ILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLT 93

                          90
                  ....*....|....*
gi 1737110181 259 SAFKKGIGETPLQYR 273
Cdd:PRK11511   94 RTFKNYFDVPPHKYR 108
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 34-76 7.60e-05

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: 39.93  E-value: 7.60e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1737110181  34 HWH-QCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKV 76
Cdd:pfam07883  14 HRHpGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRF 57
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 193-273 1.64e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 42.22  E-value: 1.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 193 LDALAAELGKSRSYVSRRFHAEtGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETPLQY 272
Cdd:PRK09978  161 LARIASELLMSPSLLKKKLREE-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEY 239


                  .
gi 1737110181 273 R 273
Cdd:PRK09978  240 Q 240
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
183-277 1.80e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 42.27  E-value: 1.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 183 LDEHYQEKFRLDALAAELGKSRSYVSRRFHAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFK 262
Cdd:PRK10572  192 ISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFK 271

                          90
                  ....*....|....*
gi 1737110181 263 KGIGETPLQYRKNHS 277
Cdd:PRK10572  272 KCTGASPSEFRARCE 286
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 190-276 2.95e-04

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 41.52  E-value: 2.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1737110181 190 KFRLDALAAELGKSRSYVSRRFhAETGEKIHDYLNTLRLRKACECLLHTDSSVRDIAAQAGFSDVTWFISAFKKGIGETP 269
Cdd:PRK15185  222 QWKLTDVADHIFMSTSTLKRKL-AEEGTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP 300


                  ....*....
gi 1737110181 270 LQYRK--NH 276
Cdd:PRK15185  301 STFIKmaNH 309
cupin_HpaA-like_N cd06999
AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain; Members ...
 18-74 1.82e-03

AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain; Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, similar to Escherichia coli 4-hydroxyphenylacetate catabolism regulatory protein HpaA (also known as 4HPA). HpaA is encoded by the hpaA gene which is located upstream of hpaBC. It is activated by 4-HPA, 3-HPA and phenylacetate, and represents a member of the AraC/XylS family of regulators that recognizes aromatic effectors. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380403 [Multi-domain]  Cd Length: 98  Bit Score: 36.71  E-value: 1.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1737110181  18 TVASFSRLFANTVRYHHWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLH 74
Cdd:cd06999    23 TIAARSRLHDWEIAPHRHADLFQVLYIESGGGEVRLDGRTHPLSAPALVVVPPGVVH 79
bicupin_oxalic TIGR03404
bicupin, oxalate decarboxylase family; Members of this protein family are defined as bicupins ...
 24-83 4.52e-03

bicupin, oxalate decarboxylase family; Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins.


Pssm-ID: 274565 [Multi-domain]  Cd Length: 367  Bit Score: 38.07  E-value: 4.52e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1737110181  24 RLFANTVRYHHWHQCLEILYVEEG-FGVAIVDN--RHY--TMRPGRLFFFPPFTLHKVM-VDEQAE 83
Cdd:TIGR03404  73 RLEPGAIRELHWHKEAEWAYVLYGsCRITAVDEngRNYidDVGAGDLWYFPPGIPHSLQgLDEGCE 138
cupin_OxDC-like cd20306
Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and ...
 21-74 4.64e-03

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.


Pssm-ID: 380440 [Multi-domain]  Cd Length: 151  Bit Score: 36.80  E-value: 4.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1737110181  21 SFSRLF--ANTVRYHHWHQ-CLEILYVEEGFG-VAIVDNR----HYTMRPGRLFFFPPFTLH 74
Cdd:cd20306    35 SIYRLRlsPGGIREPHWHPnANELGYVISGEArVSILDPTgsldTFTVKPGQVVFIPQGWLH 96
cupin_YbfI-like_N cd07001
AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal ...
 34-92 6.23e-03

AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, 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, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380405 [Multi-domain]  Cd Length: 76  Bit Score: 34.67  E-value: 6.23e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1737110181  34 HWHQCLEILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLHKVMVDEQAEAIYRRTIIH 92
Cdd:cd07001    18 HFHDFYVIGFIESGQRTLFCEGKEYTVEPGDLLLINPRDVHSCIQISGRRLDYERINIW 76
cupin_MmsR-like_N cd06986
AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain; This ...
 41-74 6.88e-03

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: 34.77  E-value: 6.88e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1737110181  41 ILYVEEGFGVAIVDNRHYTMRPGRLFFFPPFTLH 74
Cdd:cd06986    31 LHYVLSGKGTFSVNGKTYHLKAGQGFLIPPGEPH 64
 
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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