254780424

254780424

transcriptional regulator protein

GeneID in NCBI database:8209410Locus tag:CLIBASIA_01545
Protein GI in NCBI database:254780424Protein Accession:YP_003064837.1
Gene range:-(331060, 331494)Protein Length:144aa
Gene description:transcriptional regulator protein
COG prediction:[K] Predicted transcriptional regulators
KEGG prediction:transcriptional regulator protein
SEED prediction:Predicted transcriptional regulator
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
TOPPREDnone 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----
MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
cccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHccccccccccHHHHHHHHHHcccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
ccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHcccccHccHHHHHHHHHHHcccHHHHHccccccccccccccccHHHHcccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHccccEEEEEHccEccc
mvgnkkipnpvdinvgkrIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVlespisfffdvsptvcsdisseennvmdfistpdglqlnryfiqIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
mvgnkkipnpvdinvgkrirLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVrsivssekkyrtieeecmveq
MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
************INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS***************DFISTPDGLQLNRYFIQIDDVKVRQKIIELVR********************
MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
*****KIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTV*******ENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVE*
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ
MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMVEQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target144 transcriptional regulator protein [Candidatus Liberibac
254781218205 hypothetical protein CLIBASIA_05625 [Candidatus Li 0.016
>gi|254781218|ref|YP_003065631.1| hypothetical protein CLIBASIA_05625 [Candidatus Liberibacter asiaticus str. psy62] Length = 205 Back     alignment
 Score = 30.0 bits (66), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 2   VGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKG 50
           V NKK  +P  I  G R++  R   GMSQ + G+ LG+    +  YE+G
Sbjct: 103 VTNKKRLDPYAI--GARLKSIRKDKGMSQIEFGKLLGMPNSTLSNYEQG 149

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

IdentityAlignment graphLength Definition Round E-value
Target144 transcriptional regulator protein [Candidatus Liberibac
315122130145 transcriptional regulator protein [Candidatus Liberibac 1 1e-55
241202771138 XRE family transcriptional regulator [Rhizobium legumin 1 2e-41
222084698139 transcriptional regulator protein [Agrobacterium radiob 1 3e-41
116250159138 HTH-type transcriptional regulator [Rhizobium leguminos 1 3e-41
190890041139 transcriptional regulator protein [Rhizobium etli CIAT 1 4e-41
90420537139 transcriptional regulator [Aurantimonas manganoxydans S 1 8e-41
227820634136 putative transcriptional regulator [Sinorhizobium fredi 1 1e-40
325291795140 transcriptional regulator [Agrobacterium sp. H13-3] Len 1 2e-40
254470793135 dna-binding protein [Pseudovibrio sp. JE062] Length = 1 1 7e-40
222147356140 transcriptional regulator [Agrobacterium vitis S4] Leng 1 1e-39
>gi|315122130|ref|YP_004062619.1| transcriptional regulator protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 145 Back     alignment and organism information
 Score =  218 bits (556), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 108/139 (77%), Positives = 119/139 (85%)

Query: 1   MVGNKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQ 60
           M+GNKK PNPVDINVGKRIRLRR ILGMSQEKLG+ LGITFQQVQKYEKGVNRVGASRLQ
Sbjct: 1   MIGNKKTPNPVDINVGKRIRLRRTILGMSQEKLGDSLGITFQQVQKYEKGVNRVGASRLQ 60

Query: 61  HISEVLESPISFFFDVSPTVCSDISSEENNVMDFISTPDGLQLNRYFIQIDDVKVRQKII 120
           +IS  L+ PISFFFD  P VCS   SEENN+MDF+S+ DGLQLNR+F QI DVKVRQKII
Sbjct: 61  NISRALDIPISFFFDDPPEVCSGALSEENNIMDFLSSSDGLQLNRHFTQIKDVKVRQKII 120

Query: 121 ELVRSIVSSEKKYRTIEEE 139
           +LV+SIVS EK    +EEE
Sbjct: 121 DLVKSIVSLEKSTIALEEE 139


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|241202771|ref|YP_002973867.1| XRE family transcriptional regulator [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 138 Back     alignment and organism information
>gi|222084698|ref|YP_002543227.1| transcriptional regulator protein [Agrobacterium radiobacter K84] Length = 139 Back     alignment and organism information
>gi|116250159|ref|YP_765997.1| HTH-type transcriptional regulator [Rhizobium leguminosarum bv. viciae 3841] Length = 138 Back     alignment and organism information
>gi|190890041|ref|YP_001976583.1| transcriptional regulator protein [Rhizobium etli CIAT 652] Length = 139 Back     alignment and organism information
>gi|90420537|ref|ZP_01228444.1| transcriptional regulator [Aurantimonas manganoxydans SI85-9A1] Length = 139 Back     alignment and organism information
>gi|227820634|ref|YP_002824604.1| putative transcriptional regulator [Sinorhizobium fredii NGR234] Length = 136 Back     alignment and organism information
>gi|325291795|ref|YP_004277659.1| transcriptional regulator [Agrobacterium sp. H13-3] Length = 140 Back     alignment and organism information
>gi|254470793|ref|ZP_05084196.1| dna-binding protein [Pseudovibrio sp. JE062] Length = 135 Back     alignment and organism information
>gi|222147356|ref|YP_002548313.1| transcriptional regulator [Agrobacterium vitis S4] Length = 140 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
Target144 transcriptional regulator protein [Candidatus Liberibac
smart0053056 smart00530, HTH_XRE, Helix-turn-helix XRE-family like p 1e-07
pfam0138155 pfam01381, HTH_3, Helix-turn-helix 6e-06
PRK09943185 PRK09943, PRK09943, DNA-binding transcriptional repress 0.004
cd0009358 cd00093, HTH_XRE, Helix-turn-helix XRE-family like prot 5e-08
COG1396120 COG1396, HipB, Predicted transcriptional regulators [Tr 9e-06
PRK09706135 PRK09706, PRK09706, transcriptional repressor DicA; Rev 4e-04
>gnl|CDD|128803 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins Back     alignment and domain information
>gnl|CDD|144828 pfam01381, HTH_3, Helix-turn-helix Back     alignment and domain information
>gnl|CDD|182158 PRK09943, PRK09943, DNA-binding transcriptional repressor PuuR; Provisional Back     alignment and domain information
>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins Back     alignment and domain information
>gnl|CDD|31586 COG1396, HipB, Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>gnl|CDD|182039 PRK09706, PRK09706, transcriptional repressor DicA; Reviewed Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 144 transcriptional regulator protein [Candidatus Liberibac
PRK09706135 transcriptional repressor DicA; Reviewed 99.85
TIGR02612150 mob_myst_A mobile mystery protein A; InterPro: IPR01343 98.43
PRK09943185 DNA-binding transcriptional repressor PuuR; Provisional 99.68
PHA0197667 helix-turn-helix protein 99.65
PRK13890119 conjugal transfer protein TrbA; Provisional 99.39
TIGR0307058 couple_hipB transcriptional regulator, y4mF family. Mem 99.38
smart0053056 HTH_XRE Helix-turn-helix XRE-family like proteins. 99.35
pfam0138155 HTH_3 Helix-turn-helix. This large family of DNA bindin 99.35
PRK08154 304 anaerobic benzoate catabolism transcriptional regulator 99.35
COG147668 Predicted transcriptional regulators [Transcription] 99.27
cd0009358 HTH_XRE Helix-turn-helix XRE-family like proteins. Prok 99.23
PRK0972688 DNA-binding transcriptional regulator HipB; Provisional 99.22
COG3620187 Predicted transcriptional regulator with C-terminal CBS 98.89
PRK06424144 transcription factor; Provisional 98.81
PRK08359175 transcription factor; Validated 98.78
PRK04140319 hypothetical protein; Provisional 98.78
COG1813165 Predicted transcription factor, homolog of eukaryotic M 98.78
PRK13355 518 bifunctional HTH-domain containing protein/aminotransfe 98.58
COG2944104 Predicted transcriptional regulator [Transcription] 98.51
COG1395313 Predicted transcriptional regulator [Transcription] 98.39
TIGR0260781 antidote_HigA addiction module antidote protein, HigA f 98.33
COG3093104 VapI Plasmid maintenance system antidote protein [Gener 98.3
COG1396120 HipB Predicted transcriptional regulators [Transcriptio 98.29
COG1709241 Predicted transcriptional regulator [Transcription] 98.2
PRK1007296 putative transcriptional regulator; Provisional 98.17
KOG3398135 consensus 98.12
COG1426 284 Predicted transcriptional regulator contains Xre-like H 98.09
pfam0702265 Phage_CI_repr Bacteriophage CI repressor helix-turn-hel 97.99
TIGR00270169 TIGR00270 conserved hypothetical protein TIGR00270; Int 97.95
PRK10856 332 hypothetical protein; Provisional 97.91
COG365573 Predicted transcriptional regulator [Transcription] 97.87
COG5499120 Predicted transcription regulator containing HTH domain 97.82
TIGR0268491 dnstrm_HI1420 probable addiction module antidote protei 97.35
COG2522119 Predicted transcriptional regulator [General function p 96.82
pfam08667146 BetR BetR domain. This family includes an N-terminal he 96.7
COG4800170 Predicted transcriptional regulator with an HTH domain 96.34
PRK02866147 cyanate hydratase; Validated 96.21
smart0035275 POU Found in Pit-Oct-Unc transcription factors. 96.13
TIGR02980229 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subf 95.81
PRK10014 342 DNA-binding transcriptional repressor MalI; Provisional 95.64
COG3636100 Predicted transcriptional regulator [Transcription] 95.64
PRK09492 315 treR trehalose repressor; Provisional 95.6
pfam0015775 Pou Pou domain - N-terminal to homeobox domain. 95.52
PHA0054282 putative Cro-like protein 95.5
PRK03975139 tfx putative transcriptional regulator; Provisional 95.17
PRK09526 342 lacI lac repressor; Reviewed 95.09
KOG3802398 consensus 94.93
COG342382 Nlp Predicted transcriptional regulator [Transcription] 94.84
pfam0035646 LacI Bacterial regulatory proteins, lacI family. 94.69
PRK11303 330 DNA-binding transcriptional regulator FruR; Provisional 94.66
PRK10401 346 DNA-binding transcriptional regulator GalS; Provisional 94.66
PRK08099 411 nicotinamide-nucleotide adenylyltransferase; Provisiona 94.57
smart0035470 HTH_LACI helix_turn _helix lactose operon repressor. 94.4
COG560691 Uncharacterized conserved small protein [Function unkno 94.38
COG2390 321 DeoR Transcriptional regulator, contains sigma factor-r 94.37
PRK10727 342 DNA-binding transcriptional regulator GalR; Provisional 94.37
PRK11041 341 DNA-binding transcriptional regulator CytR; Provisional 94.28
PRK1034490 DNA-binding transcriptional regulator Nlp; Provisional 94.11
PRK10703 335 DNA-binding transcriptional repressor PurR; Provisional 94.09
PRK10339 327 DNA-binding transcriptional repressor EbgR; Provisional 94.0
COG1609 333 PurR Transcriptional regulators [Transcription] 93.99
pfam08965117 DUF1870 Domain of unknown function (DUF1870). This doma 93.92
TIGR00721142 tfx DNA-binding protein, Tfx family; InterPro: IPR00464 93.79
COG1356143 tfx Transcriptional regulator [DNA replication, recombi 93.65
COG419796 Uncharacterized protein conserved in bacteria, prophage 93.51
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family; InterPro 93.27
TIGR01950142 SoxR redox-sensitive transcriptional activator SoxR; In 93.04
PRK08558238 adenine phosphoribosyltransferase; Provisional 92.9
pfam04814177 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus 92.65
PRK10423 327 transcriptional repressor RbsR; Provisional 92.55
COG1191247 FliA DNA-directed RNA polymerase specialized sigma subu 92.51
pfam02001100 DUF134 Protein of unknown function DUF134. This family 92.15
PRK07773868 replicative DNA helicase; Validated 91.93
cd0139252 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of t 91.77
PHA0067578 hypothetical protein 91.64
COG1513151 CynS Cyanate lyase [Inorganic ion transport and metabol 91.56
COG2973103 TrpR Trp operon repressor [Transcription] 91.51
pfam0533969 DUF739 Protein of unknown function (DUF739). This famil 91.3
COG2842 297 Uncharacterized ATPase, putative transposase [General f 91.26
PRK12529178 RNA polymerase sigma factor; Provisional 91.07
PRK0138199 Trp operon repressor; Provisional 90.9
PRK04217110 hypothetical protein; Provisional 90.36
TIGR02846228 spore_sigmaK RNA polymerase sigma-K factor; InterPro: I 96.21
TIGR0132195 TrpR trp operon repressor; InterPro: IPR013335 The Trp 93.65
pfam07037122 DUF1323 Putative transcription regulator (DUF1323). Thi 93.38
TIGR02885231 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR 93.36
KOG1168385 consensus 92.51
pfam0137188 Trp_repressor Trp repressor protein. This protein binds 92.5
PRK11179153 DNA-binding transcriptional regulator AsnC; Provisional 91.84
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and related 91.64
TIGR02835234 spore_sigmaE RNA polymerase sigma-E factor; InterPro: I 91.25
pfam0454550 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 lik 90.5
>PRK09706 transcriptional repressor DicA; Reviewed Back     alignment and domain information
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not Back     alignment and domain information
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional Back     alignment and domain information
>PHA01976 helix-turn-helix protein Back     alignment and domain information
>PRK13890 conjugal transfer protein TrbA; Provisional Back     alignment and domain information
>TIGR03070 couple_hipB transcriptional regulator, y4mF family Back     alignment and domain information
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins Back     alignment and domain information
>pfam01381 HTH_3 Helix-turn-helix Back     alignment and domain information
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed Back     alignment and domain information
>COG1476 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins Back     alignment and domain information
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional Back     alignment and domain information
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription] Back     alignment and domain information
>PRK06424 transcription factor; Provisional Back     alignment and domain information
>PRK08359 transcription factor; Validated Back     alignment and domain information
>PRK04140 hypothetical protein; Provisional Back     alignment and domain information
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription] Back     alignment and domain information
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional Back     alignment and domain information
>COG2944 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG1395 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids Back     alignment and domain information
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only] Back     alignment and domain information
>COG1396 HipB Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>COG1709 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK10072 putative transcriptional regulator; Provisional Back     alignment and domain information
>KOG3398 consensus Back     alignment and domain information
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown] Back     alignment and domain information
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain Back     alignment and domain information
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria Back     alignment and domain information
>PRK10856 hypothetical protein; Provisional Back     alignment and domain information
>COG3655 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG5499 Predicted transcription regulator containing HTH domain [Transcription] Back     alignment and domain information
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids Back     alignment and domain information
>COG2522 Predicted transcriptional regulator [General function prediction only] Back     alignment and domain information
>pfam08667 BetR BetR domain Back     alignment and domain information
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription] Back     alignment and domain information
>PRK02866 cyanate hydratase; Validated Back     alignment and domain information
>smart00352 POU Found in Pit-Oct-Unc transcription factors 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
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional Back     alignment and domain information
>COG3636 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK09492 treR trehalose repressor; Provisional Back     alignment and domain information
>pfam00157 Pou Pou domain - N-terminal to homeobox domain Back     alignment and domain information
>PHA00542 putative Cro-like protein Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>PRK09526 lacI lac repressor; Reviewed Back     alignment and domain information
>KOG3802 consensus Back     alignment and domain information
>COG3423 Nlp Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>pfam00356 LacI Bacterial regulatory proteins, lacI family Back     alignment and domain information
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional Back     alignment and domain information
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional Back     alignment and domain information
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional Back     alignment and domain information
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor Back     alignment and domain information
>COG5606 Uncharacterized conserved small protein [Function unknown] Back     alignment and domain information
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription] Back     alignment and domain information
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional Back     alignment and domain information
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional Back     alignment and domain information
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional Back     alignment and domain information
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional Back     alignment and domain information
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional Back     alignment and domain information
>COG1609 PurR Transcriptional regulators [Transcription] Back     alignment and domain information
>pfam08965 DUF1870 Domain of unknown function (DUF1870) 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
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair] Back     alignment and domain information
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown] 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
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211 SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer Back     alignment and domain information
>PRK08558 adenine phosphoribosyltransferase; Provisional Back     alignment and domain information
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus Back     alignment and domain information
>PRK10423 transcriptional repressor RbsR; Provisional Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>pfam02001 DUF134 Protein of unknown function DUF134 Back     alignment and domain information
>PRK07773 replicative DNA helicase; Validated Back     alignment and domain information
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators Back     alignment and domain information
>PHA00675 hypothetical protein Back     alignment and domain information
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism] Back     alignment and domain information
>COG2973 TrpR Trp operon repressor [Transcription] Back     alignment and domain information
>pfam05339 DUF739 Protein of unknown function (DUF739) Back     alignment and domain information
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only] Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK01381 Trp operon repressor; Provisional Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional 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
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression Back     alignment and domain information
>pfam07037 DUF1323 Putative transcription regulator (DUF1323) Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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
>KOG1168 consensus Back     alignment and domain information
>pfam01371 Trp_repressor Trp repressor protein Back     alignment and domain information
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional 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
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 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
>pfam04545 Sigma70_r4 Sigma-70, region 4 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
Target144 transcriptional regulator protein [Candidatus Liberibac
1y7y_A74 High-Resolution Crystal Structure Of The Restrictio 8e-04
3ivp_A126 The Structure Of A Possible Transposon-Related Dna- 0.001
1y9q_A192 Crystal Structure Of Hth_3 Family Transcriptional R 0.004
>gi|61680543|pdb|1Y7Y|A Chain A, High-Resolution Crystal Structure Of The Restriction- Modification Controller Protein C.Ahdi From Aeromonas Hydrophila Length = 74 Back     alignment and structure
 Score = 47.1 bits (110), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 26/62 (41%)

Query: 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72
          +  G+R+R  R   G+SQE L    G+    V   E+G   V    +  ++  L+     
Sbjct: 12 VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE 71

Query: 73 FF 74
           F
Sbjct: 72 LF 73


>gi|259090355|pdb|3IVP|A Chain A, The Structure Of A Possible Transposon-Related Dna-Binding Protein From Clostridium Difficile 630. Length = 126 Back     alignment and structure
>gi|60594530|pdb|1Y9Q|A Chain A, Crystal Structure Of Hth_3 Family Transcriptional Regulator From Vibrio Cholerae Length = 192 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target144 transcriptional regulator protein [Candidatus Liberibac
3eus_A86 DNA-binding protein; structural genomics, PSI2,MCSG, pr 1e-10
1y7y_A74 C.AHDI; helix-turn-helix, DNA-binding protein, transcri 3e-10
2wiu_B88 HTH-type transcriptional regulator HIPB; transferase tr 4e-10
3mlf_A111 Transcriptional regulator; structural genomics, helix-t 2e-09
2r1j_L68 Repressor protein C2; protein-DNA complex, helix-turn-h 2e-09
2b5a_A77 C.BCLI; helix-turn-helix motif, gene regulation; 1.54A 2e-09
1adr_A76 P22 C2 repressor; transcription regulation; NMR {Bacter 3e-09
1r69_A69 Repressor protein CI; gene regulating protein; 2.00A {P 6e-09
2qfc_A 293 PLCR protein; TPR, HTH, transcription regulation; 2.60A 6e-09
3kxa_A141 NGO0477 protein, putative uncharacterized protein; NEW 1e-08
1lmb_392 Protein (lambda repressor); protein-DNA complex, double 2e-08
1x57_A91 Endothelial differentiation-related factor 1; HMBF1alph 3e-08
2jvl_A107 TRMBF1; coactivator, helix-turn-helix, protein binding, 4e-08
3f6w_A83 XRE-family like protein; helix-turn-helix, DNA binding 4e-08
3clc_A82 Regulatory protein; protein-DNA complex, transcriptiona 5e-08
1y9q_A192 Transcriptional regulator, HTH_3 family; transcriptiona 6e-08
2l49_A99 C protein; P2 bacteriophage, P2 C, direct repeats, DNA- 6e-08
3kz3_A80 Repressor protein CI; five helix bundle, DNA-binding, t 7e-08
2ef8_A84 C.ECOT38IS, putative transcription factor; helix-turn-h 2e-07
2bnm_A198 Epoxidase; oxidoreductase, cupin, HTH, cation-dependant 3e-07
1utx_A66 CYLR2; DNA-binding protein, transcriptional repressor, 3e-07
3omt_A73 Uncharacterized protein; structural genomics, PSI-2, pr 4e-07
3g5g_A99 Regulatory protein; transcriptional regulator, helix-tu 1e-06
1zug_A71 Phage 434 CRO protein; gene regulating protein, transcr 1e-06
2auw_A170 Hypothetical protein NE0471; alpha-beta structure, stru 4e-06
2ppx_A99 AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif 1e-05
3bdn_A236 Lambda repressor; repressor, allostery; HET: DNA; 3.91A 2e-05
3b7h_A78 Prophage LP1 protein 11; structural genomics, PSI2, MCS 1e-04
3fmy_A73 HTH-type transcriptional regulator MQSA (YGIT/B3021); h 4e-04
3f52_A117 CLP gene regulator (CLGR); helix-turn-helix motif, tran 4e-04
3gn5_A133 HTH-type transcriptional regulator MQSA (YGIT/B3021); Z 7e-04
2ict_A94 Antitoxin HIGA; helix-turn-helix, structural genomics, 0.001
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; HTH- 0.002
3cec_A104 Putative antidote protein of plasmid maintenance system 0.003
3op9_A114 PLI0006 protein; structural genomics, PSI-2, protein st 4e-09
2p5t_A158 Putative transcriptional regulator PEZA; postsegregatio 6e-09
3ivp_A126 Putative transposon-related DNA-binding protein; APC626 8e-08
1b0n_A111 Protein (SINR protein); transcription regulator, antago 3e-07
2awi_A 317 PRGX; repressor, pheromone, DNA binding, regulatory dom 5e-06
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomics; 1.80A {Silicibacter pomeroyi} Length = 86 Back     alignment and structure
 Score = 61.0 bits (148), Expect = 1e-10
 Identities = 15/65 (23%), Positives = 24/65 (36%)

Query: 4  NKKIPNPVDINVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHIS 63
           K +  P  + + +R+R  R+  G++Q  L E L      V K E    R+         
Sbjct: 4  TKTLRTPEHVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWM 63

Query: 64 EVLES 68
             E 
Sbjct: 64 AACEG 68


>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3 Length = 74 Back     alignment and structure
>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, bacterial persistence, serine kinase, mercury derivative, SAD; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* Length = 88 Back     alignment and structure
>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp} Length = 111 Back     alignment and structure
>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 68 Back     alignment and structure
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 Length = 77 Back     alignment and structure
>1adr_A P22 C2 repressor; transcription regulation; NMR {Bacteriophage P22} SCOP: a.35.1.2 Length = 76 Back     alignment and structure
>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A Length = 69 Back     alignment and structure
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovarisraelensis atcc 35646} Length = 293 Back     alignment and structure
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, structural genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141 Back     alignment and structure
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A* Length = 92 Back     alignment and structure
>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Length = 91 Back     alignment and structure
>2jvl_A TRMBF1; coactivator, helix-turn-helix, protein binding, transcription; NMR {Trichoderma reesei} Length = 107 Back     alignment and structure
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response element family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} Length = 83 Back     alignment and structure
>3clc_A Regulatory protein; protein-DNA complex, transcriptional regulator, helix-turn- helix, DNA-bending, plasmid, transcription regulator/DNA complex; 2.80A {Enterobacter SP} Length = 82 Back     alignment and structure
>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15 Length = 192 Back     alignment and structure
>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A Length = 99 Back     alignment and structure
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} Length = 80 Back     alignment and structure
>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2} Length = 84 Back     alignment and structure
>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A Length = 198 Back     alignment and structure
>1utx_A CYLR2; DNA-binding protein, transcriptional repressor, regulation of cytolysin operon, helix-turn-helix; 1.90A {Enterococcus faecalis} SCOP: a.35.1.3 PDB: 2gzu_A Length = 66 Back     alignment and structure
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73 Back     alignment and structure
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A Length = 99 Back     alignment and structure
>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L* Length = 71 Back     alignment and structure
>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1 Length = 170 Back     alignment and structure
>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3 Length = 99 Back     alignment and structure
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236 Back     alignment and structure
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1} Length = 78 Back     alignment and structure
>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12} Length = 73 Back     alignment and structure
>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional activator, human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A Length = 117 Back     alignment and structure
>3gn5_A HTH-type transcriptional regulator MQSA (YGIT/B3021); Zn-binding protein, HTH-XRE DNA binding motif, DNA-binding, transcription regulation; HET: MEQ; 2.15A {Escherichia coli k-12} PDB: 3gn5_B* Length = 133 Back     alignment and structure
>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium; 1.63A {Escherichia coli CFT073} SCOP: a.35.1.3 PDB: 2icp_A Length = 94 Back     alignment and structure
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* Length = 133 Back     alignment and structure
>3cec_A Putative antidote protein of plasmid maintenance system; ZP_00107635.1, structural genomics, joint center for structural genomics; HET: MSE; 1.60A {Nostoc punctiforme pcc 73102} Length = 104 Back     alignment and structure
>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Length = 114 Back     alignment and structure
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, helix-turn-helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae TIGR4} Length = 158 Back     alignment and structure
>3ivp_A Putative transposon-related DNA-binding protein; APC62618, structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile 630} Length = 126 Back     alignment and structure
>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 Length = 111 Back     alignment and structure
>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain, transcription; 2.25A {Enterococcus faecalis} SCOP: a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A 2grl_A 2grm_A Length = 317 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target144 transcriptional regulator protein [Candidatus Liberibac
3ivp_A126 Putative transposon-related DNA-binding protein; APC626 99.73
3op9_A114 PLI0006 protein; structural genomics, PSI-2, protein st 99.67
2bnm_A198 Epoxidase; oxidoreductase, cupin, HTH, cation-dependant 99.67
2ewt_A71 BLDD, putative DNA-binding protein; the DNA-binding dom 99.65
1y9q_A192 Transcriptional regulator, HTH_3 family; transcriptiona 99.64
1b0n_A111 Protein (SINR protein); transcription regulator, antago 99.63
2b5a_A77 C.BCLI; helix-turn-helix motif, gene regulation; 1.54A 99.6
2kpj_A94 SOS-response transcriptional repressor, LEXA; NESG, GFT 99.6
2r1j_L68 Repressor protein C2; protein-DNA complex, helix-turn-h 99.58
1adr_A76 P22 C2 repressor; transcription regulation; NMR {Entero 99.58
3f52_A117 CLP gene regulator (CLGR); helix-turn-helix motif, tran 99.58
2ict_A94 Antitoxin HIGA; helix-turn-helix, structural genomics, 99.58
3b7h_A78 Prophage LP1 protein 11; structural genomics, PSI2, MCS 99.57
2p5t_A158 Putative transcriptional regulator PEZA; postsegregatio 99.56
1y7y_A74 C.AHDI; helix-turn-helix, DNA-binding protein, transcri 99.56
3g5g_A99 Regulatory protein; transcriptional regulator, helix-tu 99.55
2jvl_A107 TRMBF1; coactivator, helix-turn-helix, Pro binding, tra 99.55
3mlf_A111 Transcriptional regulator; structural genomics, helix-t 99.55
3cec_A104 Putative antidote protein of plasmid maintenance system 99.54
1r69_A69 Repressor protein CI; gene regulating protein; 2.00A {P 99.54
1zug_A71 Phage 434 CRO protein; gene regulating protein, transcr 99.53
3omt_A73 Uncharacterized protein; structural genomics, PSI-2, pr 99.52
3clc_A82 Regulatory protein; protein-DNA complex, transcriptiona 99.52
2wiu_B88 HTH-type transcriptional regulator HIPB; transferase tr 99.52
3bs3_A76 Putative DNA-binding protein; XRE-family, structural ge 99.52
3f6w_A83 XRE-family like protein; helix-turn-helix, DNA binding 99.52
1utx_A66 CYLR2; DNA-binding protein, transcriptional repressor, 99.51
3eus_A86 DNA-binding protein; structural genomics, PSI2,MCSG, pr 99.49
3kxa_A141 NGO0477 protein, putative uncharacterized protein; NEW 99.48
1x57_A91 Endothelial differentiation-related factor 1; HMBF1alph 99.47
2l49_A99 C protein; P2 bacteriophage, P2 C, direct repeats, DNA- 99.47
2ofy_A86 Putative XRE-family transcriptional regulator; transcri 99.46
1lmb_392 Protein (lambda repressor); protein-DNA complex, double 99.46
3kz3_A80 Repressor protein CI; five helix bundle, DNA-binding, t 99.45
2awi_A 317 PRGX; repressor, pheromone, DNA binding, regulatory dom 99.39
3bdn_A236 Lambda repressor; repressor, allostery; HET: DNA; 3.91A 99.36
2ef8_A84 C.ECOT38IS, putative transcription factor; helix-turn-h 99.36
2qfc_A 293 PLCR protein; TPR, HTH, transcription regulation; 2.60A 99.34
2a6c_A83 Helix-turn-helix motif; putative transcriptional regula 99.32
2eby_A113 Putative HTH-type transcriptional regulator YBAQ; hypot 99.25
3fmy_A73 HTH-type transcriptional regulator MQSA (YGIT/B3021); h 99.25
3g7d_A443 PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic 99.22
2fjr_A189 Repressor protein CI; genetic switch, regulation, coope 99.16
2wus_R112 RODZ, putative uncharacterized protein; structural prot 99.13
2ppx_A99 AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif 99.08
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; HTH- 99.01
3fym_A130 Putative uncharacterized protein; HTH DNA binding, DNA 98.88
2o38_A120 Hypothetical protein; alpha-beta, helix-turn-helix, str 98.87
2auw_A170 Hypothetical protein NE0471; alpha-beta structure, stru 98.76
1dw9_A156 Cyanate lyase; cyanate degradation, structural genomics 98.28
3bd1_A79 CRO protein; transcription factor, helix-turn-helix, pr 96.7
2k9q_A77 Uncharacterized protein; all helix, helix-turn-helix, p 96.17
1neq_A74 DNA-binding protein NER; NMR {Enterobacteria phage MU} 95.84
1uxc_A65 FRUR (1-57), fructose repressor; DNA-binding protein, L 95.62
3kjx_A 344 Transcriptional regulator, LACI family; LACL family, pr 95.58
2hsg_A 332 Glucose-resistance amylase regulator; CCPA, transcripti 95.02
2w48_A 315 Sorbitol operon regulator; SORC, activator, repressor, 94.79
3h5t_A 366 Transcriptional regulator, LACI family; DNA-dependent, 94.69
1r71_A178 Transcriptional repressor protein KORB; INCP, plasmid p 94.57
1zs4_A83 Regulatory protein CII; helix-turn-helix, transcription 94.49
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription factor, 94.12
1qpz_A 340 PURA, protein (purine nucleotide synthesis repressor); 93.94
2ox6_A166 Hypothetical protein SO3848; structural genomics, PSI-2 93.53
3e3m_A 355 Transcriptional regulator, LACI family; structural geno 92.82
3h5o_A 339 Transcriptional regulator GNTR; transcription regulator 92.47
1s4k_A120 Putative cytoplasmic protein YDIL; structural genomics, 92.37
1rzs_A61 Antirepressor, regulatory protein CRO; helix-turn-helix 91.87
3bil_A 348 Probable LACI-family transcriptional regulator; structu 91.72
1vz0_A230 PARB, chromosome partitioning protein PARB; nuclear pro 91.26
1jye_A 349 Lactose operon repressor; gene regulation, protein stab 91.0
3dbi_A 338 Sugar-binding transcriptional regulator, LACI family; s 90.71
1zx4_A192 P1 PARB, plasmid partition PAR B protein, PARB; transla 96.86
3mky_B189 Protein SOPB; partition, F plasmid, centromere, DNA bin 95.22
1jhf_A202 LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {E 94.37
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated reco 92.7
1jhg_A101 Trp operon repressor; complex (regulatory protein/pepti 92.23
3frw_A107 Putative Trp repressor protein; structural genomics, AP 91.74
2r0q_C209 Putative transposon TN552 DNA-invertase BIN3; site-spec 91.2
1u78_A141 TC3 transposase, transposable element TC3 transposase; 91.13
3kor_A119 Possible Trp repressor; putative DNA-binding Trp repres 90.75
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein struct 90.41
>3ivp_A Putative transposon-related DNA-binding protein; APC62618, structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile 630} Back     alignment and structure
Probab=99.73  E-value=3.5e-17  Score=128.86  Aligned_cols=114  Identities=17%  Similarity=0.185  Sum_probs=84.3

Q ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCHHHHHHH
Q ss_conf             99999999999819979999998724699999985289883589999999754999999506774431111101454211
Q gi|254780424|r   14 NVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVSPTVCSDISSEENNVMD   93 (144)
Q Consensus        14 ~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~~~~~~~~~~~~~~~~~   93 (144)
                      +||++||.+|+.+||||++||..+|||.++|++||+|.+.|+.++|.+||++|+||++|||........+          
T Consensus        12 ~ig~rlk~~R~~~gltq~elA~~lgvs~s~is~~E~G~~~ps~~~l~~ia~~l~v~~~~l~~~~~~~~~~----------   81 (126)
T 3ivp_A           12 ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFFLPASSQVKS----------   81 (126)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHHTCCSHHHHSCCCCCCCC----------
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCC----------
T ss_conf             9999999999984999999967309998799999707779999999999999796899982888754353----------


Q ss_pred             HHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2038678999999872899999999999999999999997539998732
Q gi|254780424|r   94 FISTPDGLQLNRYFIQIDDVKVRQKIIELVRSIVSSEKKYRTIEEECMV  142 (144)
Q Consensus        94 ~~~~~e~~~l~~~~~~l~~~~~r~~i~~l~~~l~~~e~~~~~~~ee~l~  142 (144)
                          .....+...+..+++. ....+..+++.+...........|++..
T Consensus        82 ----~~~~~l~~~~~~l~~~-~~~~i~~i~~~~~~~~e~~e~~~e~l~~  125 (126)
T 3ivp_A           82 ----TKRRQLENKIDNFTDA-DLVIMESVADGIVKSKEVGEMAGENLYF  125 (126)
T ss_dssp             ----HHHHHHHHHTTTCCHH-HHHHHHHHHHHHHHHHHHHC--------
T ss_pred             ----HHHHHHHHHHHCCCHH-HHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             ----7999999999749999-9999999999999807777614651101



>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Back     alignment and structure
>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A Back     alignment and structure
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor A3} Back     alignment and structure
>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15 Back     alignment and structure
>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 Back     alignment and structure
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 Back     alignment and structure
>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Back     alignment and structure
>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L Back     alignment and structure
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Back     alignment and structure
>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional activator, human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A Back     alignment and structure
>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli CFT073} SCOP: a.35.1.3 PDB: 2icp_A Back     alignment and structure
>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1} Back     alignment and structure
>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, helix-turn-helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae TIGR4} Back     alignment and structure
>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3 Back     alignment and structure
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A Back     alignment and structure
>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Back     alignment and structure
>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp} Back     alignment and structure
>3cec_A Putative antidote protein of plasmid maintenance system; ZP_00107635.1, structural genomics, joint center for structural genomics; HET: MSE; 1.60A {Nostoc punctiforme pcc 73102} Back     alignment and structure
>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A Back     alignment and structure
>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L* Back     alignment and structure
>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Back     alignment and structure
>3clc_A Regulatory protein; protein-DNA complex, transcriptional regulator, helix-turn- helix, DNA-bending, plasmid, transcription regulator/DNA complex; 2.80A {Enterobacter SP} Back     alignment and structure
>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, bacterial persistence, serine kinase, mercury derivative, SAD; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* Back     alignment and structure
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis nctc 9343} Back     alignment and structure
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response element family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} Back     alignment and structure
>1utx_A CYLR2; DNA-binding protein, transcriptional repressor, regulation of cytolysin operon, helix-turn-helix; 1.90A {Enterococcus faecalis} SCOP: a.35.1.3 PDB: 2gzu_A Back     alignment and structure
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomics; 1.80A {Silicibacter pomeroyi} Back     alignment and structure
>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Back     alignment and structure
>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Back     alignment and structure
>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A Back     alignment and structure
>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PSI, protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3 Back     alignment and structure
>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A* Back     alignment and structure
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} Back     alignment and structure
>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain, transcription; 2.25A {Enterococcus faecalis} SCOP: a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A 2grl_A 2grm_A Back     alignment and structure
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Back     alignment and structure
>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2} Back     alignment and structure
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovarisraelensis atcc 35646} Back     alignment and structure
>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13 Back     alignment and structure
>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli} Back     alignment and structure
>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12} Back     alignment and structure
>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A Back     alignment and structure
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A Back     alignment and structure
>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima} Back     alignment and structure
>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3 Back     alignment and structure
>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* Back     alignment and structure
>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp} Back     alignment and structure
>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.83A {Rhodopseudomonas palustris CGA009} SCOP: a.35.1.13 Back     alignment and structure
>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein structure initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1 Back     alignment and structure
>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: SO4; 1.65A {Escherichia coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A 2iu7_A 2iv1_A 2iuo_A 2ivg_A Back     alignment and structure
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution; 1.40A {Xylella fastidiosa ann-1} Back     alignment and structure
>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron} Back     alignment and structure
>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A Back     alignment and structure
>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transcription regulation; NMR {Escherichia coli K12} SCOP: a.35.1.5 PDB: 1uxd_A Back     alignment and structure
>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi} Back     alignment and structure
>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A Back     alignment and structure
>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae} Back     alignment and structure
>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum} Back     alignment and structure
>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1 Back     alignment and structure
>1zs4_A Regulatory protein CII; helix-turn-helix, transcription activator, transcription/DNA complex; HET: DNA; 1.70A {Enterobacteria phage lambda} SCOP: a.35.1.9 Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ... Back     alignment and structure
>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, protein structure initiative, midwest center for structural genomics; 1.70A {Shewanella oneidensis mr-1} SCOP: a.35.1.6 Back     alignment and structure
>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi} Back     alignment and structure
>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum} Back     alignment and structure
>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, protein structure initiative; 1.90A {Salmonella typhimurium LT2} SCOP: a.35.1.6 Back     alignment and structure
>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Back     alignment and structure
>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032} Back     alignment and structure
>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1 Back     alignment and structure
>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ... Back     alignment and structure
>3dbi_A Sugar-binding transcriptional regulator, LACI family; structural genomics, protein structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12} Back     alignment and structure
>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A Back     alignment and structure
>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A* Back     alignment and structure
>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 1jhc_A 1jhe_A 1lea_A 1leb_A Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure
>1jhg_A Trp operon repressor; complex (regulatory protein/peptide), DNA-binding regulatory protein; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 1trr_A* 1tro_A* Back     alignment and structure
>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, protein structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A Back     alignment and structure
>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus} Back     alignment and structure
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Back     alignment and structure
>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus} Back     alignment and structure
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19 Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 144 transcriptional regulator protein [Candidatus Liberibac
d1y7ya169 a.35.1.3 (A:5-73) Restriction-modification controller p 1e-10
d2b5aa177 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus c 9e-10
d1b0na268 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {B 3e-09
d2r1jl166 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain 2e-08
d1y9qa179 a.35.1.8 (A:4-82) Probable transcriptional regulator VC 2e-08
d1r69a_63 a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bac 8e-08
d1utxa_66 a.35.1.3 (A:) Putative transcription regulator CylR2 {E 1e-07
d2croa_65 a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712] 3e-06
d1lmb3_87 a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain { 4e-06
d2ppxa162 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agr 1e-05
d2auwa167 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-term 2e-05
d1x57a178 a.35.1.12 (A:8-85) Endothelial differentiation-related 3e-05
d2ofya182 a.35.1.3 (A:3-84) Putative transcriptional regulator RH 0.001
>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]} Length = 69 Back     information, alignment and structure

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]
 Score = 59.4 bits (144), Expect = 1e-10
 Identities = 16/62 (25%), Positives = 26/62 (41%)

Query: 13 INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISF 72
          +  G+R+R  R   G+SQE L    G+    V   E+G   V    +  ++  L+     
Sbjct: 8  VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE 67

Query: 73 FF 74
           F
Sbjct: 68 LF 69


>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Length = 77 Back     information, alignment and structure
>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Length = 68 Back     information, alignment and structure
>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} Length = 66 Back     information, alignment and structure
>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]} Length = 79 Back     information, alignment and structure
>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]} Length = 63 Back     information, alignment and structure
>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} Length = 66 Back     information, alignment and structure
>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]} Length = 65 Back     information, alignment and structure
>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]} Length = 87 Back     information, alignment and structure
>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Length = 62 Back     information, alignment and structure
>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Length = 67 Back     information, alignment and structure
>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78 Back     information, alignment and structure
>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]} Length = 82 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target144 transcriptional regulator protein [Candidatus Liberibac
d2b5aa177 Regulatory protein C.BclI {Bacillus caldolyticus [TaxId 99.59
d2r1jl166 P22 C2 repressor, DNA-binding domain {Salmonella bacter 99.57
d1b0na268 SinR repressor, DNA-binding domain {Bacillus subtilis [ 99.57
d1y9qa179 Probable transcriptional regulator VC1968, N-terminal d 99.57
d1y7ya169 Restriction-modification controller protein C.AhdI {Aer 99.56
d2croa_65 cro 434 {Bacteriophage 434 [TaxId: 10712]} 99.54
d1r69a_63 434 C1 repressor, DNA-binding domain {Bacteriophage 434 99.53
d1utxa_66 Putative transcription regulator CylR2 {Enterococcus fa 99.52
d1lmb3_87 lambda C1 repressor, DNA-binding domain {Bacteriophage 99.47
d2icta187 Antitoxin HigA {Escherichia coli [TaxId: 562]} 99.47
d1x57a178 Endothelial differentiation-related factor 1, EDF1 {Hum 99.47
d2ofya182 Putative transcriptional regulator RHA1_ro04071 {Rhodoc 99.46
d2o38a189 Hypothetical protein RPA3824 {Rhodopseudomonas palustri 99.38
d2a6ca169 HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 99.29
d2ppxa162 Uncharacterized protein Atu1735 {Agrobacterium tumefaci 99.1
d2auwa167 Hypothetical protein NE0471 C-terminal domain {Nitrosom 98.82
d2bnma171 Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal 97.44
d1dwka186 Cyanase N-terminal domain {Escherichia coli [TaxId: 562 97.14
d2awia165 PrgX {Enterococcus faecalis [TaxId: 1351]} 96.79
d1e3oc275 Oct-1 {Human (Homo sapiens) [TaxId: 9606]} 96.3
d1au7a272 Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]} 95.72
d2hsga157 Glucose-resistance amylase regulator CcpA, N-terminal d 95.36
d1ic8a294 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo s 95.35
d1efaa159 Lac repressor (LacR), N-terminal domain {Escherichia co 95.21
d1r71a_114 Transcriptional repressor protein KorB DNA-binding doma 94.9
d1qpza157 Purine repressor (PurR), N-terminal domain {Escherichia 94.73
d1nera_74 Ner {Bacteriophage mu [TaxId: 10677]} 94.57
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Escherich 93.77
d2ox6a1162 Hypothetical protein SO3848 {Shewanella oneidensis [Tax 93.64
d1s4ka_120 Putative cytoplasmic protein YdiL {Salmonella typhimuri 93.37
d1hlva166 DNA-binding domain of centromere binding protein B (CEN 92.68
d1jhga_101 Trp repressor, TrpR {Escherichia coli [TaxId: 562]} 92.21
d1vz0a193 Putative partitioning protein ParB/Spo0J {Thermus therm 94.86
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 93.08
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 92.46
>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Back     information, alignment and structure
class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]
Probab=99.59  E-value=3.3e-15  Score=114.69  Aligned_cols=70  Identities=24%  Similarity=0.419  Sum_probs=64.0

Q ss_pred             CCHHH--HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf             99899--99999999999981997999999872469999998528988358999999975499999950677
Q gi|254780424|r    8 PNPVD--INVGKRIRLRRMILGMSQEKLGECLGITFQQVQKYEKGVNRVGASRLQHISEVLESPISFFFDVS   77 (144)
Q Consensus         8 ~~~~d--~~iG~rIr~~R~~~glTQ~eLA~~lGvs~s~is~~E~G~~~ps~~~L~~iA~~l~v~~~~l~~~~   77 (144)
                      .|.+|  ..+|++||.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.|.+||.+|||++++||...
T Consensus         2 ~~~~~~~~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~l~~~~   73 (77)
T d2b5aa1           2 INEIEIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFRKM   73 (77)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCC
T ss_conf             863899999999999999980999999998979799999999869989999999999999698999985423



>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} Back     information, alignment and structure
>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]} Back     information, alignment and structure
>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]} Back     information, alignment and structure
>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]} Back     information, alignment and structure
>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} Back     information, alignment and structure
>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]} Back     information, alignment and structure
>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]} Back     information, alignment and structure
>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]} Back     information, alignment and structure
>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure
>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Back     information, alignment and structure
>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure
>d2bnma1 a.35.1.3 (A:6-76) Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain {Streptomyces wedmorensis [TaxId: 43759]} Back     information, alignment and structure
>d1dwka1 a.35.1.4 (A:1-86) Cyanase N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2awia1 a.35.1.11 (A:2-66) PrgX {Enterococcus faecalis [TaxId: 1351]} Back     information, alignment and structure
>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]} Back     information, alignment and structure
>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]} Back     information, alignment and structure
>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2ox6a1 a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]} Back     information, alignment and structure
>d1s4ka_ a.35.1.6 (A:) Putative cytoplasmic protein YdiL {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 144 transcriptional regulator protein [Candidatus Libe
3eus_A_86 (A:) DNA-binding protein; structural genomics, PSI 6e-12
3f6w_A_