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Conserved domains on  [gi|694064532|ref|WP_032411019|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Klebsiella]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10054599)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

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];
74-122 1.52e-11

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.52e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
FliA super family cl34170
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-102 1.00e-03

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


The actual alignment was detected with superfamily member COG1191:

Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 37.50  E-value: 1.00e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 694064532  44 IPYESDIYDDVMLPGEVCDVMHKENF-SLQAAWRIL-------------RGMSQQEVAEKLGISQSAVSQLEA 102
Cdd:COG1191  152 LEDGDDLLDLLESGDPEEELEHEELReALAEAIEQLpererlvlslyyfEELTLKEIAEVLGVSESRVSRLHK 224
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
74-122 1.52e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.52e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 74-122 9.36e-11

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: 53.71  E-value: 9.36e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
73-122 5.22e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.36  E-value: 5.22e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 694064532    73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:smart00530   3 KELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 73-122 1.63e-09

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: 50.23  E-value: 1.63e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 694064532   73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:pfam01381   2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
73-120 5.01e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 38.24  E-value: 5.01e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 694064532  73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYG 120
Cdd:PRK09943  13 SEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYG 60
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-102 1.00e-03

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 37.50  E-value: 1.00e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 694064532  44 IPYESDIYDDVMLPGEVCDVMHKENF-SLQAAWRIL-------------RGMSQQEVAEKLGISQSAVSQLEA 102
Cdd:COG1191  152 LEDGDDLLDLLESGDPEEELEHEELReALAEAIEQLpererlvlslyyfEELTLKEIAEVLGVSESRVSRLHK 224
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 75-116 1.01e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 1.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 694064532   75 WRILRGMSQQEVAEKLGISQSAVSQLealdsrpQKRTREKLA 116
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRR-------LKRARKKLR 155
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
74-122 1.52e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.16  E-value: 1.52e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:COG1396   14 ELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 74-122 9.36e-11

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: 53.71  E-value: 9.36e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
74-126 3.31e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 52.54  E-value: 3.31e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 694064532  74 AWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCTQEQI 126
Cdd:COG1476   11 ELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
73-122 5.22e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.36  E-value: 5.22e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 694064532    73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:smart00530   3 KELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 73-122 1.63e-09

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: 50.23  E-value: 1.63e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 694064532   73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:pfam01381   2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 76-122 1.59e-08

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: 48.01  E-value: 1.59e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 694064532  76 RILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCT 122
Cdd:COG1813   21 REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 52-128 8.71e-08

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: 46.94  E-value: 8.71e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 694064532  52 DDVMLPgevcDVMH-KENFSLQAAWRILR---GMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYGCTQEQIS 127
Cdd:COG3620    2 RDLMSR----DVVTvSPDDTLGEALRLMRkelGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77


                 .
gi 694064532 128 L 128
Cdd:COG3620   78 V 78
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
79-99 3.22e-07

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 45.20  E-value: 3.22e-07
                         10        20
                 ....*....|....*....|.
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQ 99
Cdd:COG2522   27 RGLSQSEIAKLLGITQAAVSQ 47
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 73-126 6.57e-07

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: 43.67  E-value: 6.57e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 694064532   73 AAWRILRGMSQQEVAEKLGISQSAVSQLEA-LDSRPQKRTREKLAAIYGCTQEQI 126
Cdd:pfam13560   7 RRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
64-119 7.56e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 38.38  E-value: 7.56e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 694064532  64 MHKENFSLQ--AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIY 119
Cdd:COG2944    1 MTKKPLTPEeiRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLE 58
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 76-115 2.02e-04

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 36.64  E-value: 2.02e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 694064532   76 RILRGMSQQEVAEKLGISQSAVSQLEaldsrpqKRTREKL 115
Cdd:pfam04545  16 RYGEGLTLEEIGERLGISRERVRQIE-------KRALRKL 48
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 71-115 2.66e-04

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 39.45  E-value: 2.66e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 694064532  71 LQAAWRILRGMSQQEVAEKLGISQSAVSQ---------LEALDSRPQKRTREKL 115
Cdd:COG3415   29 LRAVLLLAEGLSVREIAERLGVSRSTVYRwlkryreggLAGLKDRPRGGRPSKL 82
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
79-100 4.41e-04

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 37.17  E-value: 4.41e-04
                         10        20
                 ....*....|....*....|..
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQL 100
Cdd:COG5606   44 RGLTQAEAAELLGITQPRVSDL 65
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
73-120 5.01e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 38.24  E-value: 5.01e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 694064532  73 AAWRILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYG 120
Cdd:PRK09943  13 SEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYG 60
DmsR COG3413
Predicted transcriptional regulator, contains HTH domain [General function prediction only];
79-99 6.99e-04

Predicted transcriptional regulator, contains HTH domain [General function prediction only];


Pssm-ID: 442639 [Multi-domain]  Cd Length: 143  Bit Score: 37.22  E-value: 6.99e-04
                         10        20
                 ....*....|....*....|.
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQ 99
Cdd:COG3413  107 REATLEELAEELGISKSTLSE 127
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 76-120 7.87e-04

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: 35.73  E-value: 7.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 694064532   76 RILRGMSQQEVAEKLGISQSAVSQLEALDSRPQKRTREKLAAIYG 120
Cdd:pfam12844   8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 75-115 8.12e-04

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 35.16  E-value: 8.12e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 694064532  75 WRILRGMSQQEVAEKLGISQSAVSQLEaldsrpqKRTREKL 115
Cdd:cd06171   21 LRFGEGLSYEEIAEILGISRSTVRQRL-------HRALKKL 54
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 44-102 1.00e-03

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 37.50  E-value: 1.00e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 694064532  44 IPYESDIYDDVMLPGEVCDVMHKENF-SLQAAWRIL-------------RGMSQQEVAEKLGISQSAVSQLEA 102
Cdd:COG1191  152 LEDGDDLLDLLESGDPEEELEHEELReALAEAIEQLpererlvlslyyfEELTLKEIAEVLGVSESRVSRLHK 224
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 75-116 1.01e-03

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 36.94  E-value: 1.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 694064532   75 WRILRGMSQQEVAEKLGISQSAVSQLealdsrpQKRTREKLA 116
Cdd:TIGR02937 121 LRYLEGLSYKEIAEILGISVGTVKRR-------LKRARKKLR 155
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 78-115 1.15e-03

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 36.89  E-value: 1.15e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 694064532  78 LRGMSQQEVAEKLGISQSavsqleALDSRPQkRTREKL 115
Cdd:PRK09637 120 LEGLSQKEIAEKLGLSLS------GAKSRVQ-RGRVKL 150
COG1356 COG1356
Transcriptional regulator [Transcription];
79-116 1.47e-03

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 36.37  E-value: 1.47e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQLEaldsrpqKRTREKLA 116
Cdd:COG1356   22 RGLTQQEIADILGTSRANVSSIE-------KSARENIE 52
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 71-102 1.80e-03

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: 34.78  E-value: 1.80e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 694064532  71 LQAAwRILRGMSQQEVAEKLGISQSAVSQLEA 102
Cdd:COG1426   10 LRQA-REAKGLSLEDVAERTKISVSYLEAIEE 40
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
76-101 2.03e-03

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 36.46  E-value: 2.03e-03
                         10        20
                 ....*....|....*....|....*.
gi 694064532  76 RILRGMSQQEVAEKLGISQSAVSQLE 101
Cdd:PRK08215 221 RFFQGKTQMEVAEEIGISQAQVSRLE 246
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 79-100 2.51e-03

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 34.78  E-value: 2.51e-03
                         10        20
                 ....*....|....*....|..
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQL 100
Cdd:COG3093   21 LGLSQTELAKALGVSRQRISEI 42
HTH_23 pfam13384
Homeodomain-like domain;
71-99 2.93e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 33.78  E-value: 2.93e-03
                          10        20
                  ....*....|....*....|....*....
gi 694064532   71 LQAAWRILRGMSQQEVAEKLGISQSAVSQ 99
Cdd:pfam13384   8 ARALLLLAEGLSVKEIAELLGVSRRTVYR 36
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
72-100 3.03e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 36.26  E-value: 3.03e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 694064532  72 QAAWR-ILRGMSQQEVAEKLGISQSAVSQL 100
Cdd:COG2390    1 RAAWLyYVEGLTQREIAERLGISRRTVSRL 30
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 73-100 3.29e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 33.72  E-value: 3.29e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 694064532   73 AAWRILR------GMSQQEVAEKLGISQSAVSQL 100
Cdd:pfam12802   6 AQFRVLLalarnpGLTVAELARRLGISKQTVSRL 39
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
75-133 4.45e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 33.58  E-value: 4.45e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 694064532  75 WRIL--RGMSQQEVAEKLGISQSAVSQLEaldSRPQKRTR----EKLAAIYGCTQEQISLYLPKE 133
Cdd:COG3655    7 DELLaeRGMTKKELAEATGISRATLSRLK---NGKAKAVRldtlEKICKALDCQPGDLLEYVPDE 68
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
71-117 5.03e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 35.50  E-value: 5.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 694064532  71 LQAAWRILRGMSQQEVAEKLGISQSAV-SQLealdsrpqKRTREKLAA 117
Cdd:COG2771  133 REVLRLLAEGLTLKEIARILGISERTVrTHL--------KRIYRKLGV 172
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
75-101 6.85e-03

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 35.15  E-value: 6.85e-03
                         10        20
                 ....*....|....*....|....*..
gi 694064532  75 WRILRGMSQQEVAEKLGISQSAVSQLE 101
Cdd:COG1709   30 WREDFGISQTELARELGVSPSVISDYE 56
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
81-101 8.17e-03

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 34.83  E-value: 8.17e-03
                         10        20
                 ....*....|....*....|.
gi 694064532  81 MSQQEVAEKLGISQSAVSQLE 101
Cdd:PRK08301 199 KTQKEVADMLGISQSYISRLE 219
tfx PRK03975
putative transcriptional regulator; Provisional
 79-116 8.54e-03

putative transcriptional regulator; Provisional


Pssm-ID: 179690 [Multi-domain]  Cd Length: 141  Bit Score: 34.10  E-value: 8.54e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 694064532  79 RGMSQQEVAEKLGISQSAVSQLEaldsrpqKRTREKLA 116
Cdd:PRK03975  20 RGLTQQEIADILGTSRANVSSIE-------KRARENIE 50
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
76-117 8.97e-03

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 34.56  E-value: 8.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 694064532  76 RILRGMSQQEVAEKLGISQSAVSQLEaldSRPQKRTREKLAA 117
Cdd:PRK05572 214 RYFKDKTQSEVAKRLGISQVQVSRLE---KKILKQMKEKLDE 252
 
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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