254780693

254780693

transcriptional regulator protein

GeneID in NCBI database:8209697Locus tag:CLIBASIA_02900
Protein GI in NCBI database:254780693Protein Accession:YP_003065106.1
Gene range:+(575763, 576470)Protein Length:235aa
Gene description:transcriptional regulator protein
COG prediction:[K] DNA-binding HTH domain-containing proteins
KEGG prediction:transcriptional regulator protein
SEED prediction:PUTATIVE TRANSCRIPTION REGULATOR PROTEIN
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED2 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-----
MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
ccccccccccccccccccHHHHHHHHHHHHHHEEEEEEccccccccccEEEEEEccccccccccHHHHHHHccHHHHHHHHHcccccccccccccccccHHHHHHHHHHHccccccEEEEEEEccccccEEEEccccHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHHccccHHHHHHHHHHccccc
cccccccccccccccHHHHHHHHHHHHHHHccccEEEEEEEcccccccccEEEcccccHHHHHHHHHcccccccHHHHHcccccccEEcccHcccccccccHHHHHHHHHHcccccEEEEEcccccccEEEEEEccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHHcccHHHHHHHHHHHccccc
msentltgkkssslqelsPRLHLIQNRIKARNFALYTINSALDFPRRQQLICElhnydldsgdipnilietygddflfhfnsgllpiIWQSIQEETVIESSgqlsvrleggllpfagiafpvrlgfhkngyviFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQlagdgytseEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
msentltgkkssslqelsPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSatvkldavNRIQAIAKAIRFGYIC
MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
********KKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFL****************ETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
***************ELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
*****LTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target235 transcriptional regulator protein [Candidatus Liberibac
254780694246 probable transcriptional regulator protein, LuxR f 1e-07
>gi|254780694|ref|YP_003065107.1| probable transcriptional regulator protein, LuxR family [Candidatus Liberibacter asiaticus str. psy62] Length = 246 Back     alignment
 Score = 48.1 bits (113), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 33/57 (57%)

Query: 174 LTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIR 230
           LT RE  CL    +G TS+EIA  LG+S +TVN Y+ S   K     R  AIA A+R
Sbjct: 186 LTGREVECLTWISEGKTSDEIAVILGISRNTVNNYIASIMRKTATKTRSGAIAYAVR 242

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target235 transcriptional regulator protein [Candidatus Liberibac
315121858235 transcriptional regulator protein [Candidatus Liberibac 1 1e-114
222084852248 transcriptional regulator protein [Agrobacterium radiob 1 2e-59
86356299248 LuxR family transcriptional regulator [Rhizobium etli C 1 4e-56
327193021306 putative transcriptional regulator protein, LuxR family 1 2e-55
190890350248 transcriptional regulator protein, LuxR family [Rhizobi 1 2e-55
218514696240 probable transcriptional regulator protein, LuxR family 1 2e-55
150395471247 response regulator receiver protein [Sinorhizobium medi 1 3e-55
82940563248 putative transcription regulator protein MotS, LuxR fam 1 6e-55
116250469248 LuxR family transcriptional regulator [Rhizobium legumi 1 2e-54
262283888248 VisR [Rhizobium leguminosarum bv. viciae] Length = 248 1 3e-54
>gi|315121858|ref|YP_004062347.1| transcriptional regulator protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 235 Back     alignment and organism information
 Score =  413 bits (1062), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 199/235 (84%), Positives = 217/235 (92%)

Query: 1   MSENTLTGKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLD 60
           MSENTL  KKS SL ELS +L +IQ RIKARNFALYTIN ALD PRRQQL+CEL+NYD +
Sbjct: 1   MSENTLLEKKSFSLLELSSKLKIIQKRIKARNFALYTINCALDSPRRQQLVCELNNYDPE 60

Query: 61  SGDIPNILIETYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAF 120
           SG+IPNILI+TYGD+FLFHFNSGLLPIIW ++QEET+IESSGQ  +RL+ G+LPFAGIAF
Sbjct: 61  SGEIPNILIKTYGDEFLFHFNSGLLPIIWNNMQEETIIESSGQFFIRLDKGILPFAGIAF 120

Query: 121 PVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLELFKKRSSAARNLTERETS 180
           P+RLGFHKNGYV+FT+E LMLANEVIIEAHGACYQVI  FL LFKKRSSAARNLTERETS
Sbjct: 121 PLRLGFHKNGYVVFTAECLMLANEVIIEAHGACYQVIMGFLALFKKRSSAARNLTERETS 180

Query: 181 CLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC 235
           CLQLAGDGYTSEEIA+KLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC
Sbjct: 181 CLQLAGDGYTSEEIAKKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYIC 235


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222084852|ref|YP_002543381.1| transcriptional regulator protein [Agrobacterium radiobacter K84] Length = 248 Back     alignment and organism information
>gi|86356299|ref|YP_468191.1| LuxR family transcriptional regulator [Rhizobium etli CFN 42] Length = 248 Back     alignment and organism information
>gi|327193021|gb|EGE59933.1| putative transcriptional regulator protein, LuxR family [Rhizobium etli CNPAF512] Length = 306 Back     alignment and organism information
>gi|190890350|ref|YP_001976892.1| transcriptional regulator protein, LuxR family [Rhizobium etli CIAT 652] Length = 248 Back     alignment and organism information
>gi|218514696|ref|ZP_03511536.1| probable transcriptional regulator protein, LuxR family [Rhizobium etli 8C-3] Length = 240 Back     alignment and organism information
>gi|150395471|ref|YP_001325938.1| response regulator receiver protein [Sinorhizobium medicae WSM419] Length = 247 Back     alignment and organism information
>gi|82940563|emb|CAJ44292.1| putative transcription regulator protein MotS, LuxR family [Rhizobium leguminosarum bv. viciae] Length = 248 Back     alignment and organism information
>gi|116250469|ref|YP_766307.1| LuxR family transcriptional regulator [Rhizobium leguminosarum bv. viciae 3841] Length = 248 Back     alignment and organism information
>gi|262283888|gb|ACY40752.1| VisR [Rhizobium leguminosarum bv. viciae] Length = 248 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target235 transcriptional regulator protein [Candidatus Liberibac
smart0042158 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon 4e-14
COG277165 COG2771, CsgD, DNA-binding HTH domain-containing protei 2e-11
pfam0019658 pfam00196, GerE, Bacterial regulatory proteins, luxR fa 6e-10
COG2909894 COG2909, MalT, ATP-dependent transcriptional regulator 3e-08
TIGR03020247 TIGR03020, EpsA, transcriptional regulator EpsA 4e-08
TIGR03541232 TIGR03541, reg_near_HchA, LuxR family transcriptional r 8e-07
PRK15369211 PRK15369, PRK15369, two component system sensor kinase 6e-04
TIGR02937158 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, si 0.002
PRK10360196 PRK10360, PRK10360, DNA-binding transcriptional activat 0.002
cd0617057 cd06170, LuxR_C_like, C-terminal DNA-binding domain of 3e-13
COG2197211 COG2197, CitB, Response regulator containing a CheY-lik 5e-11
>gnl|CDD|128698 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon Back     alignment and domain information
>gnl|CDD|32632 COG2771, CsgD, DNA-binding HTH domain-containing proteins [Transcription] Back     alignment and domain information
>gnl|CDD|109261 pfam00196, GerE, Bacterial regulatory proteins, luxR family Back     alignment and domain information
>gnl|CDD|32733 COG2909, MalT, ATP-dependent transcriptional regulator [Transcription] Back     alignment and domain information
>gnl|CDD|163106 TIGR03020, EpsA, transcriptional regulator EpsA Back     alignment and domain information
>gnl|CDD|132580 TIGR03541, reg_near_HchA, LuxR family transcriptional regulatory, chaperone HchA-associated Back     alignment and domain information
>gnl|CDD|185267 PRK15369, PRK15369, two component system sensor kinase SsrB; Provisional Back     alignment and domain information
>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA; Provisional Back     alignment and domain information
>gnl|CDD|99777 cd06170, LuxR_C_like, C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 235 transcriptional regulator protein [Candidatus Liberibac
PRK13870234 transcriptional regulator TraR; Provisional 100.0
PRK10188240 DNA-binding transcriptional activator SdiA; Provisional 100.0
TIGR03541232 reg_near_HchA LuxR family transcriptional regulatory, c 100.0
TIGR03020247 EpsA transcriptional regulator EpsA. Proteins in this f 99.85
PRK04841903 transcriptional regulator MalT; Provisional 99.78
PRK09483216 response regulator; Provisional 99.75
PRK09935210 transcriptional regulator FimZ; Provisional 99.73
PRK10100216 DNA-binding transcriptional regulator CsgD; Provisional 99.73
PRK10840216 transcriptional regulator RcsB; Provisional 99.72
PRK10651216 transcriptional regulator NarL; Provisional 99.72
PRK09390202 fixJ response regulator FixJ; Provisional 99.71
COG2197211 CitB Response regulator containing a CheY-like receiver 99.71
PRK09958204 DNA-binding transcriptional activator EvgA; Provisional 99.71
PRK10403215 transcriptional regulator NarP; Provisional 99.69
PRK10360196 DNA-binding transcriptional activator UhpA; Provisional 99.68
COG2909894 MalT ATP-dependent transcriptional regulator [Transcrip 99.68
pfam0019658 GerE Bacterial regulatory proteins, luxR family. 99.59
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR-like 99.56
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (ac 99.52
PRK11475205 DNA-binding transcriptional activator BglJ; Provisional 99.5
COG4566202 TtrR Response regulator [Signal transduction mechanisms 99.38
COG277165 CsgD DNA-binding HTH domain-containing proteins [Transc 99.38
TIGR02985167 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bactero 98.46
PRK06930170 positive control sigma-like factor; Validated 98.2
pfam07638185 Sigma70_ECF ECF sigma factor. These proteins are probab 98.16
PRK12523172 RNA polymerase sigma factor; Reviewed 98.16
TIGR02937162 sigma70-ECF RNA polymerase sigma factor, sigma-70 famil 98.1
PRK08295209 RNA polymerase factor sigma-70; Validated 98.08
PRK12527159 RNA polymerase sigma factor; Reviewed 98.07
PRK07037183 extracytoplasmic-function sigma-70 factor; Validated 98.07
PRK12525168 RNA polymerase sigma factor; Provisional 98.05
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 98.04
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 98.01
PRK11922231 RNA polymerase sigma factor; Provisional 98.01
PRK13919187 putative RNA polymerase sigma E protein; Provisional 97.99
PRK09645171 RNA polymerase sigma factor SigL; Provisional 97.98
PRK09047161 RNA polymerase factor sigma-70; Validated 97.98
PRK12519194 RNA polymerase sigma factor; Provisional 97.96
PRK09651172 RNA polymerase sigma factor FecI; Provisional 97.96
PRK09652192 RNA polymerase sigma factor RpoE; Provisional 97.96
PRK09638177 RNA polymerase sigma factor SigY; Reviewed 97.94
PRK09639166 RNA polymerase sigma factor SigX; Provisional 97.94
PRK12515189 RNA polymerase sigma factor; Provisional 97.94
PRK12526206 RNA polymerase sigma factor; Provisional 97.93
PRK05602186 RNA polymerase sigma factor; Reviewed 97.93
PRK12524196 RNA polymerase sigma factor; Provisional 97.93
PRK12537184 RNA polymerase sigma factor; Provisional 97.93
pfam0828154 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 l 97.92
PRK12516190 RNA polymerase sigma factor; Provisional 97.91
PRK12529178 RNA polymerase sigma factor; Provisional 97.91
PRK12512184 RNA polymerase sigma factor; Provisional 97.91
PRK12541161 RNA polymerase sigma factor; Provisional 97.9
PRK12543190 RNA polymerase sigma factor; Provisional 97.9
PRK12514179 RNA polymerase sigma factor; Provisional 97.89
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C- 97.88
PRK09641187 RNA polymerase sigma factor SigW; Provisional 97.86
PRK09643197 RNA polymerase sigma factor SigM; Reviewed 97.86
PRK12547164 RNA polymerase sigma factor; Provisional 97.86
PRK12528167 RNA polymerase sigma factor; Provisional 97.85
PRK12534187 RNA polymerase sigma factor; Provisional 97.85
PRK12538233 RNA polymerase sigma factor; Provisional 97.85
PRK12517188 RNA polymerase sigma factor; Provisional 97.82
PRK12513194 RNA polymerase sigma factor; Provisional 97.82
PRK12542185 RNA polymerase sigma factor; Provisional 97.81
PRK11924180 RNA polymerase sigma factor; Provisional 97.81
PRK09648187 RNA polymerase sigma factor SigD; Reviewed 97.81
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 97.81
PRK09647222 RNA polymerase sigma factor SigE; Reviewed 97.8
PRK12531194 RNA polymerase sigma factor; Provisional 97.79
PRK06811185 RNA polymerase factor sigma-70; Validated 97.78
PRK12539184 RNA polymerase sigma factor; Provisional 97.76
PRK12533217 RNA polymerase sigma factor; Provisional 97.76
PRK12522173 RNA polymerase sigma factor; Provisional 97.76
PRK09644165 RNA polymerase sigma factor SigM; Provisional 97.75
PRK12520191 RNA polymerase sigma factor; Provisional 97.74
PRK12536178 RNA polymerase sigma factor; Provisional 97.73
PRK12546188 RNA polymerase sigma factor; Provisional 97.73
PRK12511182 RNA polymerase sigma factor; Provisional 97.73
PRK12518175 RNA polymerase sigma factor; Provisional 97.72
PRK09640188 RNA polymerase sigma factor SigX; Reviewed 97.7
PRK12540181 RNA polymerase sigma factor; Provisional 97.69
PRK09415177 RNA polymerase factor sigma C; Reviewed 97.69
PRK06759154 RNA polymerase factor sigma-70; Validated 97.68
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 97.66
PRK12535195 RNA polymerase sigma factor; Provisional 97.64
PRK12532195 RNA polymerase sigma factor; Provisional 97.61
PRK09649185 RNA polymerase sigma factor SigC; Reviewed 97.61
PRK12544207 RNA polymerase sigma factor; Provisional 97.61
PRK12530191 RNA polymerase sigma factor; Provisional 97.55
COG3413215 Predicted DNA binding protein [General function predict 97.55
COG1595182 RpoE DNA-directed RNA polymerase specialized sigma subu 97.51
pfam0454550 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 lik 97.45
pfam0496753 HTH_10 HTH DNA binding domain. 97.35
PRK12545201 RNA polymerase sigma factor; Provisional 97.24
PRK09636 289 RNA polymerase sigma factor SigJ; Provisional 97.19
PRK13558674 bacterio-opsin activator; Provisional 97.14
TIGR02983165 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E 97.14
PRK08583257 RNA polymerase sigma factor SigB; Validated 97.1
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 97.04
TIGR02999194 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family 97.02
PRK07670250 RNA polymerase sigma factor SigD; Validated 96.97
PRK07122263 RNA polymerase sigma factor SigF; Reviewed 96.96
PRK12427229 flagellar biosynthesis sigma factor; Provisional 96.94
TIGR01884231 cas_HTH CRISPR locus-related DNA-binding protein; Inter 96.84
PRK08215257 sporulation sigma factor SigG; Reviewed 96.81
TIGR02952171 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 f 96.8
PRK05572251 sporulation sigma factor SigF; Validated 96.8
PRK07500289 rpoH2 RNA polymerase factor sigma-32; Reviewed 96.76
PRK06288261 RNA polymerase sigma factor WhiG; Reviewed 96.74
PRK08301239 sporulation sigma factor SigE; Reviewed 96.74
PRK05803228 sporulation sigma factor SigK; Reviewed 96.68
PRK06596284 RNA polymerase factor sigma-32; Reviewed 96.67
PRK09635 290 sigI RNA polymerase sigma factor SigI; Provisional 96.66
PRK06986234 fliA flagellar biosynthesis sigma factor; Validated 96.66
PRK10336219 DNA-binding transcriptional regulator QseB; Provisional 96.57
PRK03975139 tfx putative transcriptional regulator; Provisional 96.56
PRK08241 341 RNA polymerase factor sigma-70; Validated 96.56
PRK05911257 RNA polymerase sigma factor sigma-28; Reviewed 96.43
PRK12423 202 LexA repressor; Provisional 96.34
PRK00215 204 LexA repressor; Validated 96.34
PRK05949327 RNA polymerase sigma factor; Validated 96.34
PRK05657328 RNA polymerase sigma factor RpoS; Validated 96.31
pfam0172665 LexA_DNA_bind LexA DNA binding domain. This is the DNA 96.3
pfam02001100 DUF134 Protein of unknown function DUF134. This family 96.29
PRK07921320 RNA polymerase sigma factor SigB; Reviewed 96.23
PRK13413200 mpi multiple promoter invertase; Provisional 96.09
PRK05901398 RNA polymerase sigma factor; Provisional 96.07
PRK09210368 RNA polymerase sigma factor RpoD; Validated 96.04
PRK07598410 RNA polymerase sigma factor SigC; Validated 96.02
PRK07406385 RNA polymerase sigma factor RpoD; Validated 95.93
COG1191247 FliA DNA-directed RNA polymerase specialized sigma subu 95.92
PRK04217110 hypothetical protein; Provisional 95.81
PRK07405318 RNA polymerase sigma factor SigD; Validated 95.81
pfam09862113 DUF2089 Protein of unknown function(DUF2089). This doma 95.74
TIGR02984190 Sig-70_plancto1 RNA polymerase sigma-70 factor, Plancto 95.68
PRK10710240 DNA-binding transcriptional regulator BaeR; Provisional 95.65
TIGR02997336 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacte 95.54
pfam0827955 HTH_11 HTH domain. This family includes helix-turn-heli 95.49
COG0856 203 Orotate phosphoribosyltransferase homologs [Nucleotide 95.17
cd0009078 HTH_ARSR Arsenical Resistance Operon Repressor and simi 95.17
TIGR02954173 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 f 95.12
COG134299 Predicted DNA-binding proteins [General function predic 95.1
TIGR02479227 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family 94.96
PRK00118105 putative DNA-binding protein; Validated 94.86
PRK13719220 conjugal transfer transcriptional regulator TraJ; Provi 94.73
pfam04297101 UPF0122 Putative helix-turn-helix protein, YlxM / p13 l 94.73
TIGR02980229 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subf 94.63
COG0568342 RpoD DNA-directed RNA polymerase, sigma subunit (sigma7 94.55
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and related 94.53
TIGR02989163 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirell 94.43
cd0038395 trans_reg_C Effector domain of response regulator. Bact 94.41
TIGR02960 329 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; 94.35
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family; InterPro 94.27
COG3415138 Transposase and inactivated derivatives [DNA replicatio 94.21
PRK10766224 DNA-binding transcriptional regulator TorR; Provisional 94.17
pfam0048677 Trans_reg_C Transcriptional regulatory protein, C termi 94.15
COG3355126 Predicted transcriptional regulator [Transcription] 94.14
PRK09468239 ompR osmolarity response regulator; Provisional 94.13
COG1710139 Uncharacterized protein conserved in archaea [Function 94.09
COG1318182 Predicted transcriptional regulators [Transcription] 93.93
pfam0279645 HTH_7 Helix-turn-helix domain of resolvase. 93.78
smart0086278 Trans_reg_C Transcriptional regulatory protein, C termi 93.72
PRK09836226 DNA-binding transcriptional activator CusR; Provisional 93.69
PRK11517223 transcriptional regulatory protein YedW; Provisional 93.69
PRK10701240 DNA-binding transcriptional regulator RstA; Provisional 93.67
PRK06704228 RNA polymerase factor sigma-70; Validated 93.65
pfam0344479 DUF293 Domain of unknown function. This domain is alway 93.6
PRK10643222 DNA-binding transcriptional regulator BasR; Provisional 93.59
PRK10955232 DNA-binding transcriptional regulator CpxR; Provisional 93.48
smart00344108 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenou 93.38
PRK11083229 DNA-binding response regulator CreB; Provisional 93.31
COG5625113 Predicted transcription regulator containing HTH domain 93.12
TIGR02941256 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014 93.11
PRK02277 201 orotate phosphoribosyltransferase-like protein; Provisi 93.05
PRK10161229 transcriptional regulator PhoB; Provisional 92.99
TIGR03001249 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcale 92.92
PRK09191 261 two-component response regulator; Provisional 92.81
CHL00148240 orf27 Ycf27; Reviewed 92.8
COG0745229 OmpR Response regulators consisting of a CheY-like rece 92.75
TIGR02846228 spore_sigmaK RNA polymerase sigma-K factor; InterPro: I 92.74
TIGR00721142 tfx DNA-binding protein, Tfx family; InterPro: IPR00464 92.64
pfam0197868 TrmB Sugar-specific transcriptional regulator TrmB. One 92.51
pfam0137188 Trp_repressor Trp repressor protein. This protein binds 92.42
COG1356143 tfx Transcriptional regulator [DNA replication, recombi 92.4
COG3398240 Uncharacterized protein conserved in archaea [Function 92.36
PRK10816223 DNA-binding transcriptional regulator PhoP; Provisional 92.31
pfam0381188 Ins_element1 Insertion element protein. 92.21
PRK10529225 DNA-binding transcriptional activator KdpE; Provisional 91.91
pfam0102247 HTH_5 Bacterial regulatory protein, arsR family. Member 91.91
smart00347101 HTH_MARR helix_turn_helix multiple antibiotic resistanc 91.56
COG1522154 Lrp Transcriptional regulators [Transcription] 91.32
pfam0104759 MarR MarR family. The Mar proteins are involved in the 91.12
COG3877122 Uncharacterized protein conserved in bacteria [Function 91.03
TIGR02957 287 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; 90.63
PRK11179153 DNA-binding transcriptional regulator AsnC; Provisional 90.56
COG2865467 Predicted transcriptional regulator containing an HTH d 90.45
PRK11173237 two-component response regulator; Provisional 90.4
TIGR02233106 Myxo_sigma_rel Myxococcus probable DNA-binding regulato 90.36
COG2522119 Predicted transcriptional regulator [General function p 90.29
pfam0846166 HTH_12 Ribonuclease R winged-helix domain. This domain 90.02
pfam03472146 Autoind_bind Autoinducer binding domain. This domain is 99.31
TIGR02859198 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR 93.98
COG2390321 DeoR Transcriptional regulator, contains sigma factor-r 93.33
PRK11557282 putative DNA-binding transcriptional regulator; Provisi 92.8
PRK11886319 biotin--protein ligase; Provisional 92.48
PRK11337293 DNA-binding transcriptional repressor RpiR; Provisional 92.0
COG1737281 RpiR Transcriptional regulators [Transcription] 91.97
pfam03965115 Pencillinase_R Penicillinase repressor. The penicillina 90.16
>PRK13870 transcriptional regulator TraR; Provisional Back     alignment and domain information
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional Back     alignment and domain information
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated Back     alignment and domain information
>TIGR03020 EpsA transcriptional regulator EpsA Back     alignment and domain information
>PRK04841 transcriptional regulator MalT; Provisional Back     alignment and domain information
>PRK09483 response regulator; Provisional Back     alignment and domain information
>PRK09935 transcriptional regulator FimZ; Provisional Back     alignment and domain information
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional Back     alignment and domain information
>PRK10840 transcriptional regulator RcsB; Provisional Back     alignment and domain information
>PRK10651 transcriptional regulator NarL; Provisional Back     alignment and domain information
>PRK09390 fixJ response regulator FixJ; Provisional Back     alignment and domain information
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Back     alignment and domain information
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional Back     alignment and domain information
>PRK10403 transcriptional regulator NarP; Provisional Back     alignment and domain information
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional Back     alignment and domain information
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription] Back     alignment and domain information
>pfam00196 GerE Bacterial regulatory proteins, luxR family Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional Back     alignment and domain information
>COG4566 TtrR Response regulator [Signal transduction mechanisms] Back     alignment and domain information
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription] Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK06930 positive control sigma-like factor; Validated Back     alignment and domain information
>pfam07638 Sigma70_ECF ECF sigma factor Back     alignment and domain information
>PRK12523 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK08295 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK12527 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PRK12525 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK11922 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09651 RNA polymerase sigma factor FecI; Provisional Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK09638 RNA polymerase sigma factor SigY; Reviewed Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>pfam08281 Sigma70_r4_2 Sigma-70, region 4 Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12512 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12543 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>cd06171 Sigma70_r4 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) Back     alignment and domain information
>PRK09641 RNA polymerase sigma factor SigW; Provisional Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12547 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12528 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12517 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12513 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12542 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>PRK09647 RNA polymerase sigma factor SigE; Reviewed Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK12539 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12522 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09644 RNA polymerase sigma factor SigM; Provisional Back     alignment and domain information
>PRK12520 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12546 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12511 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09640 RNA polymerase sigma factor SigX; Reviewed Back     alignment and domain information
>PRK12540 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09415 RNA polymerase factor sigma C; Reviewed Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed Back     alignment and domain information
>PRK12535 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12532 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09649 RNA polymerase sigma factor SigC; Reviewed Back     alignment and domain information
>PRK12544 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>COG3413 Predicted DNA binding protein [General function prediction only] Back     alignment and domain information
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Back     alignment and domain information
>pfam04545 Sigma70_r4 Sigma-70, region 4 Back     alignment and domain information
>pfam04967 HTH_10 HTH DNA binding domain Back     alignment and domain information
>PRK12545 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09636 RNA polymerase sigma factor SigJ; Provisional Back     alignment and domain information
>PRK13558 bacterio-opsin activator; Provisional Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK07670 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster Back     alignment and domain information
>PRK08215 sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>PRK08241 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PRK12423 LexA repressor; Provisional Back     alignment and domain information
>PRK00215 LexA repressor; Validated Back     alignment and domain information
>PRK05949 RNA polymerase sigma factor; Validated Back     alignment and domain information
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>pfam01726 LexA_DNA_bind LexA DNA binding domain Back     alignment and domain information
>pfam02001 DUF134 Protein of unknown function DUF134 Back     alignment and domain information
>PRK07921 RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>PRK13413 mpi multiple promoter invertase; Provisional Back     alignment and domain information
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information
>PRK07406 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>pfam09862 DUF2089 Protein of unknown function(DUF2089) Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional Back     alignment and domain information
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>pfam08279 HTH_11 HTH domain Back     alignment and domain information
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism] Back     alignment and domain information
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors Back     alignment and domain information
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>COG1342 Predicted DNA-binding proteins [General function prediction only] Back     alignment and domain information
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional Back     alignment and domain information
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like Back     alignment and domain information
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>cd00383 trans_reg_C Effector domain of response regulator Back     alignment and domain information
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis Back     alignment and domain information
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional Back     alignment and domain information
>pfam00486 Trans_reg_C Transcriptional regulatory protein, C terminal Back     alignment and domain information
>COG3355 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK09468 ompR osmolarity response regulator; Provisional Back     alignment and domain information
>COG1710 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>COG1318 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase Back     alignment and domain information
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal Back     alignment and domain information
>PRK09836 DNA-binding transcriptional activator CusR; Provisional Back     alignment and domain information
>PRK11517 transcriptional regulatory protein YedW; Provisional Back     alignment and domain information
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional Back     alignment and domain information
>PRK06704 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>pfam03444 DUF293 Domain of unknown function Back     alignment and domain information
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional Back     alignment and domain information
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional Back     alignment and domain information
>smart00344 HTH_ASNC helix_turn_helix ASNC type Back     alignment and domain information
>PRK11083 DNA-binding response regulator CreB; Provisional Back     alignment and domain information
>COG5625 Predicted transcription regulator containing HTH domain [Transcription] Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional Back     alignment and domain information
>PRK10161 transcriptional regulator PhoB; Provisional Back     alignment and domain information
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK09191 two-component response regulator; Provisional Back     alignment and domain information
>CHL00148 orf27 Ycf27; Reviewed Back     alignment and domain information
>COG0745 OmpR Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription] Back     alignment and domain information
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea Back     alignment and domain information
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB Back     alignment and domain information
>pfam01371 Trp_repressor Trp repressor protein Back     alignment and domain information
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair] Back     alignment and domain information
>COG3398 Uncharacterized protein conserved in archaea [Function unknown] Back     alignment and domain information
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional Back     alignment and domain information
>pfam03811 Ins_element1 Insertion element protein Back     alignment and domain information
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional Back     alignment and domain information
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family Back     alignment and domain information
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein Back     alignment and domain information
>COG1522 Lrp Transcriptional regulators [Transcription] Back     alignment and domain information
>pfam01047 MarR MarR family Back     alignment and domain information
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown] Back     alignment and domain information
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; InterPro: IPR014303 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional Back     alignment and domain information
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription] Back     alignment and domain information
>PRK11173 two-component response regulator; Provisional Back     alignment and domain information
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein Back     alignment and domain information
>COG2522 Predicted transcriptional regulator [General function prediction only] Back     alignment and domain information
>pfam08461 HTH_12 Ribonuclease R winged-helix domain Back     alignment and domain information
>pfam03472 Autoind_bind Autoinducer binding domain Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] Back     alignment and domain information
>PRK11557 putative DNA-binding transcriptional regulator; Provisional Back     alignment and domain information
>PRK11886 biotin--protein ligase; Provisional Back     alignment and domain information
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional Back     alignment and domain information
>COG1737 RpiR Transcriptional regulators [Transcription] Back     alignment and domain information
>pfam03965 Pencillinase_R Penicillinase repressor Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target235 transcriptional regulator protein [Candidatus Liberibac
3qp6_A265 Crystal Structure Of Cvir (Chromobacterium Violaceu 8e-32
3qp5_A265 Crystal Structure Of Cvir Bound To Antagonist Chlor 8e-31
2q0o_A236 Crystal Structure Of An Anti-Activation Complex In 1e-25
1l3l_A234 Crystal Structure Of A Bacterial Quorum-Sensing Tra 9e-24
1fse_A74 Crystal Structure Of The Bacillus Subtilis Regulato 3e-18
2rnj_A91 Nmr Structure Of The S. Aureus Vrar Dna Binding Dom 4e-18
3c3w_A225 Crystal Structure Of The Mycobacterium Tuberculosis 5e-15
1zlk_A95 Crystal Structure Of The Mycobacterium Tuberculosis 4e-14
1zlj_A78 Crystal Structure Of The Mycobacterium Tuberculosis 9e-13
3clo_A258 Crystal Structure Of Putative Transcriptional Regul 3e-12
3kln_A225 Vibrio Cholerae Vpst Length = 225 1e-15
1yio_A208 Crystallographic Structure Of Response Regulator St 3e-12
3ix3_A173 Lasr-Oc12 Hsl Complex Length = 173 3e-13
2avx_A171 Solution Structure Of E Coli Sdia1-171 Length = 171 3e-13
2uv0_E175 Structure Of The P. Aeruginosa Lasr Ligand-Binding 4e-12
gi|327200688|pdb|3QP6|A Chain A, Crystal Structure Of Cvir (Chromobacterium Violaceum 12472) Bound To C6-Hsl Length = 265 Back     alignment and structure
 Score =  141 bits (355), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 36/224 (16%), Positives = 71/224 (31%), Gaps = 5/224 (2%)

Query: 11  SSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIE 70
             +  EL   L  I ++  +    L           ++       +Y  D  +  +    
Sbjct: 34  IETEGELKAFLDNILSQAPSDRIILVLGRLNNQNQIQRMEKVLNVSYPSDWLNQYSQENF 93

Query: 71  TYGDDFLFHFNSGLLPIIWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPV-RLGFHKN 129
              D  +   + G  P+IW   +      S  +  +         +GI F       +  
Sbjct: 94  AQHDPIMR-IHLGQGPVIW-EERFSRAKGSEEKRFIAEASSNGMGSGITFSAASDRNNVG 151

Query: 130 GYVIFTSEFLMLANEVIIEAHGACYQVITDFLELF--KKRSSAARNLTERETSCLQLAGD 187
             +    +       ++   +     +    + +      S +   L++RE         
Sbjct: 152 SILSIGGKEPGRNAALVAMLNCLTPHLHQAAVRIANLPPASPSNMPLSQREYDIFHWMSR 211

Query: 188 GYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRF 231
           G T+ EIA  L +S  TV  ++ +   KL+A NR  AI   +  
Sbjct: 212 GKTNWEIATILNISERTVKFHVANVIRKLNANNRTHAIVLGMHL 255


>gi|327200684|pdb|3QP5|A Chain A, Crystal Structure Of Cvir Bound To Antagonist Chlorolactone (Cl) Length = 265 Back     alignment and structure
gi|158429605|pdb|2Q0O|A Chain A, Crystal Structure Of An Anti-Activation Complex In Bacterial Quorum Sensing Length = 236 Back     alignment and structure
>gi|21730643|pdb|1L3L|A Chain A, Crystal Structure Of A Bacterial Quorum-Sensing Transcription Factor Complexed With Pheromone And Dna Length = 234 Back     alignment and structure
gi|13786948|pdb|1FSE|A Chain A, Crystal Structure Of The Bacillus Subtilis Regulatory Protein Gere Length = 74 Back     alignment and structure
>gi|166007196|pdb|2RNJ|A Chain A, Nmr Structure Of The S. Aureus Vrar Dna Binding Domain Length = 91 Back     alignment and structure
>gi|185177925|pdb|3C3W|A Chain A, Crystal Structure Of The Mycobacterium Tuberculosis Hypoxic Response Regulator Dosr Length = 225 Back     alignment and structure
>gi|88191939|pdb|1ZLK|A Chain A, Crystal Structure Of The Mycobacterium Tuberculosis Hypoxic Response Regulator Dosr C-Terminal Domain-Dna Complex Length = 95 Back     alignment and structure
>gi|88191931|pdb|1ZLJ|A Chain A, Crystal Structure Of The Mycobacterium Tuberculosis Hypoxic Response Regulator Dosr C-Terminal Domain Length = 78 Back     alignment and structure
>gi|171849138|pdb|3CLO|A Chain A, Crystal Structure Of Putative Transcriptional Regulator Containing A Luxr Dna Binding Domain (Np_811094.1) From Bacteroides Thetaiotaomicron Vpi-5482 At 2.04 A Resolution Length = 258 Back     alignment and structure
>gi|288563091|pdb|3KLN|A Chain A, Vibrio Cholerae Vpst Length = 225 Back     alignment and structure
>gi|78100993|pdb|1YIO|A Chain A, Crystallographic Structure Of Response Regulator Styr From Pseudomonas Fluorescens Length = 208 Back     alignment and structure
>gi|258588733|pdb|3IX3|A Chain A, Lasr-Oc12 Hsl Complex Length = 173 Back     alignment and structure
>gi|110590832|pdb|2AVX|A Chain A, Solution Structure Of E Coli Sdia1-171 Length = 171 Back     alignment and structure
>gi|145580560|pdb|2UV0|E Chain E, Structure Of The P. Aeruginosa Lasr Ligand-Binding Domain Bound To Its Autoinducer Length = 175 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target235 transcriptional regulator protein [Candidatus Liberibac
2q0o_A236 Probable transcriptional activator protein TRAR; helix- 3e-16
1l3l_A234 Transcriptional activator protein TRAR; helix-turn-heli 6e-16
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial regul 4e-14
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA bindi 4e-15
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type domain, 3e-14
2krf_A73 Transcriptional regulatory protein COMA; activator, com 2e-13
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-turn-hel 7e-13
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcriptio 1e-12
1je8_A82 Nitrate/nitrite response regulator protein NARL; protei 3e-12
2jpc_A61 SSRB; DNA binding protein, structural genomics, PSI-2, 1e-11
3c57_A95 Two component transcriptional regulatory protein DEVR; 2e-11
3c3w_A225 Two component transcriptional regulatory protein DEVR; 3e-10
3klo_A225 Transcriptional regulator VPST; REC domain, HTH domain, 9e-10
1a04_A215 Nitrate/nitrite response regulator protein NARL; signal 3e-06
1yio_A208 Response regulatory protein; transcription regulation, 1e-04
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Length = 236 Back     alignment and structure
 Score = 80.7 bits (198), Expect = 3e-16
 Identities = 31/122 (25%), Positives = 50/122 (40%), Gaps = 4/122 (3%)

Query: 117 GIAFPVRLGFHKNGYVIFTSEFLMLANEVIIEAHGACYQVITDFLEL----FKKRSSAAR 172
           G+  PV   +     + F S    +    +++   A   ++    +L     K   +  +
Sbjct: 115 GVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIAAKTVLNPKQ 174

Query: 173 NLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFG 232
            L+ RE  CL  A  G T+   A   G++  TV  YL  A  KLDA +  Q +A A   G
Sbjct: 175 MLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRG 234

Query: 233 YI 234
            +
Sbjct: 235 LV 236


>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A* Length = 234 Back     alignment and structure
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Length = 258 Back     alignment and structure
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Length = 99 Back     alignment and structure
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Length = 91 Back     alignment and structure
>2krf_A Transcriptional regulatory protein COMA; activator, competence, DNA-binding, transcription regulation component regulatory system; NMR {Bacillus subtilis} Length = 73 Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Length = 79 Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Length = 74 Back     alignment and structure
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Length = 82 Back     alignment and structure
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} Length = 61 Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Length = 95 Back     alignment and structure
>3c3w_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 2.20A {Mycobacterium tuberculosis} Length = 225 Back     alignment and structure
>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A* Length = 225 Back     alignment and structure
>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A Length = 215 Back     alignment and structure
>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A Length = 208 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target235 transcriptional regulator protein [Candidatus Liberibac
2q0o_A236 Probable transcriptional activator protein TRAR; helix- 100.0
1l3l_A234 Transcriptional activator protein TRAR; helix-turn-heli 100.0
3c3w_A225 Two component transcriptional regulatory protein DEVR; 99.7
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial regul 99.7
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcriptio 99.69
3klo_A225 Transcriptional regulator VPST; REC domain, HTH domain, 99.66
2krf_A73 Transcriptional regulatory protein COMA; activator, com 99.66
1je8_A82 Nitrate/nitrite response regulator protein NARL; protei 99.65
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type domain, 99.65
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA bindi 99.64
3c57_A95 Two component transcriptional regulatory protein DEVR; 99.63
1a04_A215 Nitrate/nitrite response regulator protein NARL; signal 99.63
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-turn-hel 99.61
2jpc_A61 SSRB; DNA binding protein, structural genomics, PSI-2, 99.55
1yio_A208 Response regulatory protein; transcription regulation, 99.43
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-helix, 98.0
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zinc bin 97.93
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042 97.84
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter recogn 97.84
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structural ge 97.63
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulation, DN 97.44
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); transcript 97.4
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc bind 97.33
1p2f_A220 Response regulator; DRRB, OMPR/PHOB, transcription; HET 97.13
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription; 1.8 97.04
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, regula 96.99
1jhf_A 202 LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {E 96.98
1kgs_A225 DRRD, DNA binding response regulator D; DNA-binding pro 96.73
1ys7_A233 Transcriptional regulatory protein PRRA; response regul 96.72
1l9z_H438 Sigma factor SIGA; helix-turn-helix, coiled-coil, trans 96.64
1l0o_C243 Sigma factor; bergerat fold, helix-turn-helix, protein 96.61
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-h 96.56
3k2z_A 196 LEXA repressor; winged helix-turn-helix, SOS system, au 96.55
2a6h_F423 RNA polymerase sigma factor RPOD; RNA polymerase holoen 96.43
2gwr_A238 DNA-binding response regulator MTRA; two-component regu 96.09
1tlh_B81 Sigma-70, RNA polymerase sigma factor RPOD; anti-sigma, 96.06
1u78_A141 TC3 transposase, transposable element TC3 transposase; 95.97
2oqr_A230 Sensory transduction protein REGX3; response regulator, 95.72
1y0u_A96 Arsenical resistance operon repressor, putative; struct 95.48
2wte_A244 CSA3; antiviral protein, viral resistance, winged helix 95.43
2d1h_A109 ST1889, 109AA long hypothetical transcriptional regulat 95.42
1j5y_A 187 Transcriptional regulator, biotin repressor family; str 95.06
3iyd_F613 RNA polymerase sigma factor RPOD; transcription, initia 94.97
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated reco 94.95
2r0q_C209 Putative transposon TN552 DNA-invertase BIN3; site-spec 94.8
2cg4_A152 Regulatory protein ASNC; DNA binding, FFRP, LRP family, 94.61
2p5v_A162 Transcriptional regulator, LRP/ASNC family; NMB0573, st 94.59
1gxq_A106 PHOB, phosphate regulon transcriptional regulatory prot 94.53
2hqr_A223 Putative transcriptional regulator; phosporylation-inde 94.5
2jzy_A112 Transcriptional regulatory protein PCOR; two-component- 94.45
2e1c_A171 Putative HTH-type transcriptional regulator PH1519; DNA 94.43
2ia0_A171 Putative HTH-type transcriptional regulator PF0864; ASN 94.4
2pn6_A150 ST1022, 150AA long hypothetical transcriptional regulat 94.23
2g9w_A138 Conserved hypothetical protein; DNA-binding domain, bac 94.22
2hwv_A121 DNA-binding response regulator VICR; essential response 94.2
2dbb_A151 Putative HTH-type transcriptional regulator PH0061; ASN 94.12
2pmu_A110 Response regulator PHOP; winged helix-TUN-HELX, transcr 94.09
1i1g_A141 Transcriptional regulator LRPA; helix-turn-helix, LRP/A 93.93
1sfx_A109 Conserved hypothetical protein AF2008; structural genom 93.8
2x4h_A139 Hypothetical protein SSO2273; transcription; 2.30A {Sul 93.78
1b9m_A 265 Protein (mode); DNA-binding, gene regulation, winged he 93.71
2k4j_A115 Putative transcriptional regulator; response regulator, 93.66
1gdt_A183 GD resolvase, protein (gamma delta resolvase); protein- 93.52
2nyx_A168 Probable transcriptional regulatory protein, RV1404; al 93.42
3frw_A107 Putative Trp repressor protein; structural genomics, AP 93.34
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sulfolob 93.29
3cuo_A99 Uncharacterized HTH-type transcriptional regulator YGAV 93.18
2w25_A150 Probable transcriptional regulatory protein; transcript 93.18
2cfx_A144 HTH-type transcriptional regulator LRPC; transcriptiona 93.1
2cyy_A151 Putative HTH-type transcriptional regulator PH1519; str 93.02
1okr_A123 MECI, methicillin resistance regulatory protein MECI; b 92.99
2z9m_A120 Response regulator YYCF; two-component system, YYCG, he 92.98
1opc_A110 OMPR, OMPRC; transcription regulation, response regulat 92.87
2v79_A135 DNA replication protein DNAD; primosome, DNA remodellin 92.83
1qbj_A81 Protein (double-stranded RNA specific adenosine deamina 92.79
1r1t_A122 Transcriptional repressor SMTB; zinc, transcriptional r 92.75
2vn2_A128 DNAD, chromosome replication initiation protein; DNA re 92.62
3kor_A119 Possible Trp repressor; putative DNA-binding Trp repres 92.54
1k78_A149 Paired box protein PAX5; paired domain, ETS domain, tra 92.45
1vz0_A230 PARB, chromosome partitioning protein PARB; nuclear pro 92.35
1r1u_A106 CZRA, repressor protein; zinc, DNA binding, transcripti 92.19
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, nati 92.1
1ku9_A152 Hypothetical protein MJ223; putative transcription fact 92.02
1s3j_A155 YUSO protein; structural genomics, MARR transcriptional 91.83
3bj6_A152 Transcriptional regulator, MARR family; helix-turn-heli 91.73
2oqg_A114 Possible transcriptional regulator, ARSR family protein 91.69
3nqo_A189 MARR-family transcriptional regulator; structural genom 91.62
3b73_A111 PHIH1 repressor-like protein; winged-helix-turn-helix, 91.56
2rdp_A150 Putative transcriptional regulator MARR; PFAM PF01047, 91.51
2fa5_A162 Transcriptional regulator MARR/EMRR family; multiple an 91.32
3boq_A160 Transcriptional regulator, MARR family; structural geno 91.18
2eth_A154 Transcriptional regulator, putative, MAR family; TM0816 91.02
2qww_A154 Transcriptional regulator, MARR family; YP_013417.1, mu 90.9
2hr3_A147 Probable transcriptional regulator; MCSG, structural ge 90.84
2nnn_A140 Probable transcriptional regulator; structural genomics 90.8
2fbk_A181 Transcriptional regulator, MARR family; winged-helix-tu 90.77
3oop_A143 LIN2960 protein; protein structure initiative, PSI-2, s 90.48
1zx4_A 192 P1 PARB, plasmid partition PAR B protein, PARB; transla 90.44
1ub9_A100 Hypothetical protein PH1061; helix-turn-helix motif, wi 90.42
3bdd_A142 Regulatory protein MARR; putative multiple antibiotic-r 90.35
3onq_A262 Regulator of polyketide synthase expression; structural 90.34
1pdn_C128 Protein (PRD paired); protein-DNA complex, double helix 90.27
2o3f_A111 Putative HTH-type transcriptional regulator YBBH; APC85 90.2
3f6v_A151 Possible transcriptional regulator, ARSR family protein 90.14
2k27_A159 Paired box protein PAX-8; paired domain, solution struc 90.12
3cdh_A155 Transcriptional regulator, MARR family; helix-turn-hlei 90.09
3f3x_A144 Transcriptional regulator, MARR family, putative; DNA b 90.08
2gxg_A146 146AA long hypothetical transcriptional regulator; wing 90.02
3ix3_A173 Transcriptional activator protein LASR; quorum sensing 99.37
2avx_A171 Regulatory protein SDIA; homoserine lactone, quorum sen 99.24
1uly_A192 Hypothetical protein PH1932; helix-turn-helix, structur 95.13
2w48_A315 Sorbitol operon regulator; SORC, activator, repressor, 93.13
3i4p_A162 Transcriptional regulator, ASNC family; PSI, structural 92.96
1bia_A321 BIRA bifunctional protein; transcription regulation; 2. 92.85
3isp_A303 HTH-type transcriptional regulator RV1985C/MT2039; ROD 91.46
3hhg_A306 Transcriptional regulator, LYSR family; transcription f 92.79
1jhg_A101 Trp operon repressor; complex (regulatory protein/pepti 92.54
3hot_A345 Transposable element mariner, complete CDS; protein-DNA 90.85
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Back     alignment and structure
Probab=100.00  E-value=4.3e-32  Score=246.39  Aligned_cols=219  Identities=18%  Similarity=0.055  Sum_probs=170.2

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCCE
Q ss_conf             98622599999999999998583785899841777873102504422787789996248744412087999996179983
Q gi|254780693|r    8 GKKSSSLQELSPRLHLIQNRIKARNFALYTINSALDFPRRQQLICELHNYDLDSGDIPNILIETYGDDFLFHFNSGLLPI   87 (235)
Q Consensus         8 ~~~~~sl~dl~~~l~~l~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~~~~~~~~~p~   87 (235)
                      -+.+.+..++...+..+.+.+++++|+|+.....        .....++|+.+|.+.|....|...||++.++.....|+
T Consensus        14 l~~a~~~~~l~~~l~~~~~~~Gf~~~~y~~~~~~--------~~~~~~~~p~~w~~~Y~~~~y~~~DP~~~~~~~~~~p~   85 (236)
T 2q0o_A           14 LEAAQDGHMIKIALRSFAHSCGYDRFAYLQKDGT--------QVRTFHSYPGPWESIYLGSDYFNIDPVLAEAKRRRDVF   85 (236)
T ss_dssp             HHHCCSHHHHHHHHHHHHHHHTCCEEEEEEEETT--------EEEEEECSCHHHHHHHHHTTGGGTCHHHHHHHHCCSCE
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCEEEEEECCCC--------CEEEEECCCHHHHHHHHHCCCCCCCHHHHHHHCCCCCC
T ss_conf             9848999999999999999819987999833887--------65787179999999999889920799999997489997


Q ss_pred             EECCHHHHCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEEECCCCCCCCHHH----HHHHHHHHHHHHHHHHHH
Q ss_conf             7310133146672136789965425855358997216887523454105887899899----999999999999999851
Q gi|254780693|r   88 IWQSIQEETVIESSGQLSVRLEGGLLPFAGIAFPVRLGFHKNGYVIFTSEFLMLANEV----IIEAHGACYQVITDFLEL  163 (235)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~  163 (235)
                      .|+..............+......+|..+|+++|+..+.+..+.+++...........    ..................
T Consensus        86 ~w~~~~~~~~~~~~~~~~~~~~~~~g~~~g~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  165 (236)
T 2q0o_A           86 FWTADAWPARGSSPLRRFRDEAISHGIRCGVTIPVEGSYGSAMMLTFASPERKVDISGVLDPKKAVQLLMMVHYQLKIIA  165 (236)
T ss_dssp             EEESTTSCCSSCCHHHHHHHHHHHTTCCEEEEEEEECGGGCEEEEEEEESSSCCCCTTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHCCCCCHHHHHHHHHHHHCCCEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76721323357779999999999769801489998237887799996158763115778999999999999999999873


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC
Q ss_conf             24678874449989999999998799978999994999889999999999980799789999999976999
Q gi|254780693|r  164 FKKRSSAARNLTERETSCLQLAGDGYTSEEIAEKLGLSVHTVNAYLGSATVKLDAVNRIQAIAKAIRFGYI  234 (235)
Q Consensus       164 ~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~hl~~i~~KLg~~nR~qava~A~~~Gli  234 (235)
                      ......+...||+||+|||+|+++|+|++|||.+|+||++||++|++||++||||+||+|||++|+++|||
T Consensus       166 ~~~~~~~~~~LT~RE~evL~l~a~G~t~~eIA~~L~iS~~TV~~h~~~i~~KLgv~nr~qava~A~~~GLI  236 (236)
T 2q0o_A          166 AKTVLNPKQMLSPREMLCLVWASKGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQLVAIAKDRGLV  236 (236)
T ss_dssp             HTCCCCGGGSCCHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             33458973439987999999986699999999996999999999999999986899999999999986899



>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A* Back     alignment and structure
>3c3w_A Two component transcriptional regulatory protein DEVR; response regulator, two-component regulatory system, DNA- binding protein; 2.20A {Mycobacterium tuberculosis} Back     alignment and structure
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulator; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Back     alignment and structure