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Conserved domains on  [gi|647340151|ref|WP_025768446|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Vibrio]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12807001)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator containing a cupin-like domain

PubMed:  10473770|15808743|10556324

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-96 1.64e-17

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.49  E-value: 1.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  16 DFINQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIVNVASNPTVNIIDKE 95
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81


                 .
gi 647340151  96 D 96
Cdd:COG1396   82 E 82
PRK09943 super family cl32436
HTH-type transcriptional regulator PuuR;
19-186 4.69e-13

HTH-type transcriptional regulator PuuR;


The actual alignment was detected with superfamily member PRK09943:

Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 64.43  E-value: 4.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV---NVASNPTVnIIDKE 95
Cdd:PRK09943   5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFsepEKPDEPQV-VINQD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  96 DIPTLwtGEHGGSAKLLagTSG-PD-----MIELWRWNMKPSEVFESAGHPQGTfelfhVESGILTLNIDGKAIELHEGQ 169
Cdd:PRK09943  84 DLIEM--GSQGVSMKLV--HNGnPNrtlamIFETYQPGTTTGERIKHQGEEIGT-----VLEGEIVLTINGQDYHLVAGQ 154

                        170
                 ....*....|....*..
gi 647340151 170 SAIAKTDVPHSYSNQAD 186
Cdd:PRK09943 155 SYAINTGIPHSFSNTSA 171
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-96 1.64e-17

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.49  E-value: 1.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  16 DFINQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIVNVASNPTVNIIDKE 95
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81


                 .
gi 647340151  96 D 96
Cdd:COG1396   82 E 82
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 23-80 5.59e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 63.73  E-value: 5.59e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  23 AARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
25-80 8.51e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.92  E-value: 8.51e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 647340151    25 RIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
19-186 4.69e-13

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 64.43  E-value: 4.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV---NVASNPTVnIIDKE 95
Cdd:PRK09943   5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFsepEKPDEPQV-VINQD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  96 DIPTLwtGEHGGSAKLLagTSG-PD-----MIELWRWNMKPSEVFESAGHPQGTfelfhVESGILTLNIDGKAIELHEGQ 169
Cdd:PRK09943  84 DLIEM--GSQGVSMKLV--HNGnPNrtlamIFETYQPGTTTGERIKHQGEEIGT-----VLEGEIVLTINGQDYHLVAGQ 154

                        170
                 ....*....|....*..
gi 647340151 170 SAIAKTDVPHSYSNQAD 186
Cdd:PRK09943 155 SYAINTGIPHSFSNTSA 171
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 124-193 1.41e-11

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: 57.65  E-value: 1.41e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  124 WRWNMKPSEVFESAGHPqGTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQADSDLVFTM 193
Cdd:pfam07883   1 GLVTLPPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 26-80 2.56e-11

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 56.39  E-value: 2.56e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 647340151   26 IKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
105-191 3.99e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.77  E-value: 3.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151 105 HGGSAKLLAgtSGPDMIELWRWNMKPSEVFESAGHPqgTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQ 184
Cdd:COG1917    9 TGVSVRVLA--DGEDELEVVRVTFEPGARTPWHSHP--GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNL 84


                 ....*..
gi 647340151 185 ADSDLVF 191
Cdd:COG1917   85 GDEPAVL 91
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 106-193 7.98e-08

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380339 [Multi-domain]  Cd Length: 90  Bit Score: 48.27  E-value: 7.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151 106 GGSAKLLAGTSGPDMIELWRWNMKP-SEVFESAGHPqgTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQ 184
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPgGSGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78


                 ....*....
gi 647340151 185 ADSDLVFTM 193
Cdd:cd02209   79 GDEPARVLW 87
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 14-81 9.39e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 44.94  E-value: 9.39e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  14 DADFInQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV 81
Cdd:PRK08154  22 EAPFL-AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLL 88
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 22-75 7.35e-05

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 39.18  E-value: 7.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 647340151   22 VAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGI 75
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGL 56
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
16-96 1.64e-17

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 73.49  E-value: 1.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  16 DFINQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIVNVASNPTVNIIDKE 95
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSE 81


                 .
gi 647340151  96 D 96
Cdd:COG1396   82 E 82
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
19-81 4.43e-14

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 64.10  E-value: 4.43e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV 81
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 23-80 5.59e-14

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 63.73  E-value: 5.59e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  23 AARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
25-80 8.51e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 62.92  E-value: 8.51e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 647340151    25 RIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
19-186 4.69e-13

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 64.43  E-value: 4.69e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV---NVASNPTVnIIDKE 95
Cdd:PRK09943   5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFsepEKPDEPQV-VINQD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  96 DIPTLwtGEHGGSAKLLagTSG-PD-----MIELWRWNMKPSEVFESAGHPQGTfelfhVESGILTLNIDGKAIELHEGQ 169
Cdd:PRK09943  84 DLIEM--GSQGVSMKLV--HNGnPNrtlamIFETYQPGTTTGERIKHQGEEIGT-----VLEGEIVLTINGQDYHLVAGQ 154

                        170
                 ....*....|....*..
gi 647340151 170 SAIAKTDVPHSYSNQAD 186
Cdd:PRK09943 155 SYAINTGIPHSFSNTSA 171
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 22-79 1.07e-11

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 58.03  E-value: 1.07e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  22 VAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVAD 79
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 124-193 1.41e-11

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: 57.65  E-value: 1.41e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  124 WRWNMKPSEVFESAGHPqGTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQADSDLVFTM 193
Cdd:pfam07883   1 GLVTLPPGESSPPHRHP-GEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 26-80 2.56e-11

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 56.39  E-value: 2.56e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 647340151   26 IKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADI 80
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 19-97 4.10e-11

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 56.95  E-value: 4.10e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIVNVASNPTVNIIDKEDI 97
Cdd:COG3620   15 DDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKLVGIITRRDL 93
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 25-84 2.37e-09

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 51.52  E-value: 2.37e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151   25 RIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIVNVA 84
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
105-191 3.99e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 51.77  E-value: 3.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151 105 HGGSAKLLAgtSGPDMIELWRWNMKPSEVFESAGHPqgTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQ 184
Cdd:COG1917    9 TGVSVRVLA--DGEDELEVVRVTFEPGARTPWHSHP--GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGVPHAFRNL 84


                 ....*..
gi 647340151 185 ADSDLVF 191
Cdd:COG1917   85 GDEPAVL 91
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
91-191 8.31e-09

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 51.56  E-value: 8.31e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  91 IIDKEDIPTLWTGEHGgsaKLLAGTSGPDMIELWRWNMKP-SEVFESAGHPQGTfELFHVESGILTLNIDGKAIELHEGQ 169
Cdd:COG3837    1 IVNLDDLPGPEAGRRY---RRLGDALGLTRLGVNLITLPPgASSSPYHAHSAEE-EFVYVLEGELTLRIGGEEYVLEPGD 76

                         90       100
                 ....*....|....*....|..
gi 647340151 170 SAIAKTDVPHSYSNQADSDLVF 191
Cdd:COG3837   77 SVGFPAGVPHRLRNRGDEPARY 98
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
107-191 4.03e-08

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 49.75  E-value: 4.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151 107 GSAKLLAgtSGPDMIELWRWNMKPSEVFESAGHPQGTfELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQAD 186
Cdd:COG0662   15 GSYEVLG--EGGERLSVKRITVPPGAELSLHVHPHRD-EFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGVPHRLRNPGD 91


                 ....*
gi 647340151 187 SDLVF 191
Cdd:COG0662   92 EPLEL 96
cupin_XRE_C cd02209
XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; ...
 106-193 7.98e-08

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380339 [Multi-domain]  Cd Length: 90  Bit Score: 48.27  E-value: 7.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151 106 GGSAKLLAGTSGPDMIELWRWNMKP-SEVFESAGHPqgTFELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQ 184
Cdd:cd02209    1 GYTYELLSPGLPGRKMEPFLVTLPPgGSGGEPYSHE--GEEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVPHRYRNP 78


                 ....*....
gi 647340151 185 ADSDLVFTM 193
Cdd:cd02209   79 GDEPARVLW 87
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 14-81 9.39e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 44.94  E-value: 9.39e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  14 DADFInQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISVADIV 81
Cdd:PRK08154  22 EAPFL-AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLL 88
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 21-80 3.10e-05

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 40.20  E-value: 3.10e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 647340151   21 AVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAAN-PSISTLCKLSAALGISVADI 80
Cdd:pfam13560   1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAER 61
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 22-75 7.35e-05

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 39.18  E-value: 7.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 647340151   22 VAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGI 75
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGL 56
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 24-81 1.28e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 39.02  E-value: 1.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 647340151  24 ARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKG------AANPSISTLCKLSAALGISVADIV 81
Cdd:COG1426    8 ELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGdfdalpGPVYVRGFLRSYARALGLDPEELL 71
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 25-81 1.66e-04

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 38.29  E-value: 1.66e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151   25 RIKEHRKRLKLSLDALSKRAGISKGMLVEVEKG-AANPSISTLCKLSAALGISVADIV 81
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGkPKRVSLDTLDKICDALGCQPGDLL 58
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
21-81 3.66e-04

DNA-binding transcriptional regulator, XRE family [Transcription];


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 37.43  E-value: 3.66e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 647340151  21 AVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKG-AANPSISTLCKLSAALGISVADIV 81
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGkAKAVRLDTLEKICKALDCQPGDLL 62
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
23-69 4.98e-04

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 37.22  E-value: 4.98e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 647340151  23 AARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKL 69
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLL 54
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 139-191 1.35e-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: 36.31  E-value: 1.35e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 647340151 139 HPQGTfELFHVESGILTLNID-GKAIELHEGQSAIAKTDVPHSYSNQADSDLVF 191
Cdd:cd02208   17 HPEQD-EIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 19-76 1.86e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.14  E-value: 1.86e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151  19 NQAVAARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGIS 76
Cdd:PRK09706   3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCS 60
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 91-180 1.88e-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: 36.29  E-value: 1.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647340151  91 IIDKEDIPTLWTGEhGGSAKLLAGtsGPDMIeLWRWNMKPSEVFESAGHP--QGTFelfhVESGILTLNIDGKAIELHEG 168
Cdd:cd02238    1 FVKWDELPWEELGP-GVRRKILAG--GEKLM-LVEVRFEKGAVVPLHSHPheQIGY----VLSGRFEFTIGGETRILKPG 72

                         90
                 ....*....|..
gi 647340151 169 QSAIAKTDVPHS 180
Cdd:cd02238   73 DSYYIPPNVPHG 84
cupin_TcmJ-like cd06991
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ...
 139-194 2.32e-03

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: 36.12  E-value: 2.32e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 647340151 139 HPQGTfELFHVESGILTLNIDGKAIELHEGQSAIAKTDVPHSYSNQADSD--LVFTMS 194
Cdd:cd06991   37 HPYSE-EFLYVVRGRLVVRVDGEPVVLEAGEALLVPRGVRHRLENAGDEParLVFHLS 93
PHA01976 PHA01976
helix-turn-helix protein
 23-77 9.48e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 33.78  E-value: 9.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 647340151  23 AARIKEHRKRLKLSLDALSKRAGISKGMLVEVEKGAANPSISTLCKLSAALGISV 77
Cdd:PHA01976   4 AIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58
 
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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