254780444

254780444

bacteriophage repressor protein C1

GeneID in NCBI database:8209430Locus tag:CLIBASIA_01645
Protein GI in NCBI database:254780444Protein Accession:YP_003064857.1
Gene range:+(354092, 354763)Protein Length:223aa
Gene description:bacteriophage repressor protein C1
COG prediction:[K] Transcription termination factor
KEGG prediction:bacteriophage repressor protein C1
SEED prediction:Phage repressor
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
TOPPRED1 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---
MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
cccccHHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHcccccccccccHHHHHHHHHHccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccEEEEEEccccccccccccEEEEccccccccccEEEEEEccccEEEEEEEEccccEEEEEEccccccccccccccEEEEEEEEEEcc
cccccHHHHHHHHHHHHHHccccHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHcccHHHHHHHHcccccccccccccEcEccccccccccccccccccccccccEEEccccccccccEEEcccccEEEEEcccccccccccccEEEEccccccccccEEEEEEccccEEEEEEEEcccccEEEEEcccccccccccHHHHHHHHHHHHHcc
MTSFSHKKIWEAIDRMAErhnltpsglarkagldptsfnkskrfgiegrnrwpsTESIFKILAATNETICQlldlpfsdgrttekkekeipllyfppsgsggffdsgvfptgnkwntvgvpeirsphngiyaiqtqdtrhktqdtsmlplyrkgdilILNSAIQvncgdrllikprtgDIVAKVLISRrgrsidlmslnccypvdtvemsDIEWIARILWASQ
mtsfshkkIWEAIDRMAERHnltpsglarkagldptsfnkskrfgiegrnrwpSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAiqtqdtrhktqdtsMLPLYRKGDILILNSAIQVNCGdrllikprtgdiVAKVLisrrgrsidlmslnCCYPVDTVEMSDIEWIARILWASQ
MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYfppsgsggffdsgvfpTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
******K*IWEAIDRMA************************************STESIFKILAATNETICQLLDL*************EIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
******KKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSK*****GRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ
MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
315122107216 bacteriophage repressor protein C1 [Candidatus Liberiba 1 7e-97
239834343227 Repressor protein C [Ochrobactrum intermedium LMG 3301] 1 6e-51
92116178210 putative phage repressor [Nitrobacter hamburgensis X14] 1 1e-50
75674664210 peptidase S24 [Nitrobacter winogradskyi Nb-255] Length 1 2e-50
15887830216 bacteriophage repressor protein C1 [Agrobacterium tumef 1 2e-50
85713691210 peptidase S24 [Nitrobacter sp. Nb-311A] Length = 210 1 3e-50
222084796221 transcriptional regulator protein [Agrobacterium radiob 1 4e-50
15964281218 putative transcription regulator protein [Sinorhizobium 1 8e-50
325291874216 bacteriophage repressor protein C1 [Agrobacterium sp. H 1 1e-49
153011349217 putative phage repressor [Ochrobactrum anthropi ATCC 49 1 2e-49
>gi|315122107|ref|YP_004062596.1| bacteriophage repressor protein C1 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 216 Back     alignment and organism information
 Score =  357 bits (916), Expect = 7e-97,   Method: Compositional matrix adjust.
 Identities = 182/223 (81%), Positives = 195/223 (87%), Gaps = 7/223 (3%)

Query: 1   MTSFSHKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFK 60
           MT FSH+KIWEAID+MA+RHNLTPSGLARKAGLDPTSFNKSKRFG+EGRNRWPSTESI K
Sbjct: 1   MTKFSHEKIWEAIDQMAKRHNLTPSGLARKAGLDPTSFNKSKRFGVEGRNRWPSTESISK 60

Query: 61  ILAATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGV 120
           IL ATNETICQ   + F + +  EKKEKEIPLL FPPS S GFFDSG FP GNKWNTVGV
Sbjct: 61  ILEATNETICQFFGILFLEEKNIEKKEKEIPLLDFPPSESSGFFDSGGFPAGNKWNTVGV 120

Query: 121 PEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDI 180
           PEIRSPHNGIYAIQ        QDTSMLPLYRKGDILILN+AIQVNCGDR+LIKP  GDI
Sbjct: 121 PEIRSPHNGIYAIQ-------IQDTSMLPLYRKGDILILNAAIQVNCGDRVLIKPHEGDI 173

Query: 181 VAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ 223
            AKVLIS+RGRSIDLMSLNCCYPVDT++ SDIEWIA+ILWASQ
Sbjct: 174 EAKVLISQRGRSIDLMSLNCCYPVDTIDASDIEWIAKILWASQ 216


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|239834343|ref|ZP_04682671.1| Repressor protein C [Ochrobactrum intermedium LMG 3301] Length = 227 Back     alignment and organism information
>gi|92116178|ref|YP_575907.1| putative phage repressor [Nitrobacter hamburgensis X14] Length = 210 Back     alignment and organism information
>gi|75674664|ref|YP_317085.1| peptidase S24 [Nitrobacter winogradskyi Nb-255] Length = 210 Back     alignment and organism information
>gi|15887830|ref|NP_353511.1| bacteriophage repressor protein C1 [Agrobacterium tumefaciens str. C58] Length = 216 Back     alignment and organism information
>gi|85713691|ref|ZP_01044681.1| peptidase S24 [Nitrobacter sp. Nb-311A] Length = 210 Back     alignment and organism information
>gi|222084796|ref|YP_002543325.1| transcriptional regulator protein [Agrobacterium radiobacter K84] Length = 221 Back     alignment and organism information
>gi|15964281|ref|NP_384634.1| putative transcription regulator protein [Sinorhizobium meliloti 1021] Length = 218 Back     alignment and organism information
>gi|325291874|ref|YP_004277738.1| bacteriophage repressor protein C1 [Agrobacterium sp. H13-3] Length = 216 Back     alignment and organism information
>gi|153011349|ref|YP_001372563.1| putative phage repressor [Ochrobactrum anthropi ATCC 49188] Length = 217 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
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
cd0652981 cd06529, S24_LexA-like, Peptidase S24 LexA-like protein 8e-07
COG2932214 COG2932, COG2932, Predicted transcriptional regulator [ 3e-30
>gnl|CDD|119397 cd06529, S24_LexA-like, Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell Back     alignment and domain information
>gnl|CDD|32756 COG2932, COG2932, Predicted transcriptional regulator [Transcription] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 223 bacteriophage repressor protein C1 [Candidatus Liberiba
COG2932214 Predicted transcriptional regulator [Transcription] 99.96
PRK00215204 LexA repressor; Validated 99.92
PRK12423202 LexA repressor; Provisional 99.91
COG1974201 LexA SOS-response transcriptional repressors (RecA-medi 99.88
TIGR00498227 lexA LexA repressor; InterPro: IPR006200 Proteolytic en 98.63
PHA00361165 cI Repressor 99.89
PRK10276139 DNA polymerase V subunit UmuD; Provisional 99.7
cd0652981 S24_LexA-like Peptidase S24 LexA-like proteins are invo 99.7
cd0646284 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase su 99.58
pfam0071767 Peptidase_S24 Peptidase S24-like. 99.53
TIGR0275490 sod_Ni_protease nickel-type superoxide dismutase matura 98.79
TIGR02227203 sigpep_I_bact signal peptidase I; InterPro: IPR000223 P 98.42
cd0653085 S26_SPase_I The S26 Type I signal peptidase (SPase; Lep 98.35
TIGR02228175 sigpep_I_arch signal peptidase I; InterPro: IPR001733 P 97.18
KOG1568174 consensus 97.13
COG0681166 LepB Signal peptidase I [Intracellular trafficking and 96.98
PRK10861 324 lsignal peptidase I; Provisional 96.9
KOG3342180 consensus 96.66
PRK09706135 transcriptional repressor DicA; Reviewed 99.31
PRK09943185 DNA-binding transcriptional repressor PuuR; Provisional 99.21
PHA0197667 helix-turn-helix protein 99.16
PRK13890119 conjugal transfer protein TrbA; Provisional 98.73
TIGR0307058 couple_hipB transcriptional regulator, y4mF family. Mem 98.7
smart0053056 HTH_XRE Helix-turn-helix XRE-family like proteins. 98.63
pfam0138155 HTH_3 Helix-turn-helix. This large family of DNA bindin 98.62
PRK0972688 DNA-binding transcriptional regulator HipB; Provisional 98.52
cd0009358 HTH_XRE Helix-turn-helix XRE-family like proteins. Prok 98.39
COG147668 Predicted transcriptional regulators [Transcription] 98.32
PRK08154304 anaerobic benzoate catabolism transcriptional regulator 98.32
COG3620187 Predicted transcriptional regulator with C-terminal CBS 98.11
pfam0702265 Phage_CI_repr Bacteriophage CI repressor helix-turn-hel 98.01
COG1813165 Predicted transcription factor, homolog of eukaryotic M 97.84
TIGR0260781 antidote_HigA addiction module antidote protein, HigA f 97.62
TIGR02612150 mob_myst_A mobile mystery protein A; InterPro: IPR01343 97.58
PRK08359175 transcription factor; Validated 97.58
PRK06424144 transcription factor; Provisional 97.57
PRK04140319 hypothetical protein; Provisional 97.56
COG1709241 Predicted transcriptional regulator [Transcription] 97.39
COG365573 Predicted transcriptional regulator [Transcription] 97.25
COG4800170 Predicted transcriptional regulator with an HTH domain 97.23
TIGR0268491 dnstrm_HI1420 probable addiction module antidote protei 97.18
COG3093104 VapI Plasmid maintenance system antidote protein [Gener 97.06
KOG3398135 consensus 97.06
COG1395313 Predicted transcriptional regulator [Transcription] 96.69
PRK13355 518 bifunctional HTH-domain containing protein/aminotransfe 96.62
COG342382 Nlp Predicted transcriptional regulator [Transcription] 96.06
PRK1034490 DNA-binding transcriptional regulator Nlp; Provisional 96.02
COG1396120 HipB Predicted transcriptional regulators [Transcriptio 95.65
COG1426284 Predicted transcriptional regulator contains Xre-like H 95.57
TIGR00270169 TIGR00270 conserved hypothetical protein TIGR00270; Int 95.5
PHA0054282 putative Cro-like protein 95.42
COG3636100 Predicted transcriptional regulator [Transcription] 95.12
pfam08667146 BetR BetR domain. This family includes an N-terminal he 94.71
PRK10856 332 hypothetical protein; Provisional 94.65
COG560691 Uncharacterized conserved small protein [Function unkno 94.47
COG2390321 DeoR Transcriptional regulator, contains sigma factor-r 93.64
PRK09526 342 lacI lac repressor; Reviewed 93.34
COG5499120 Predicted transcription regulator containing HTH domain 93.27
PRK02866147 cyanate hydratase; Validated 93.03
PRK10014 342 DNA-binding transcriptional repressor MalI; Provisional 92.97
cd0476249 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of t 92.32
PRK09492 315 treR trehalose repressor; Provisional 91.29
PRK10339 327 DNA-binding transcriptional repressor EbgR; Provisional 91.04
pfam02001100 DUF134 Protein of unknown function DUF134. This family 91.0
PRK11303 330 DNA-binding transcriptional regulator FruR; Provisional 90.54
pfam0035646 LacI Bacterial regulatory proteins, lacI family. 90.31
COG2944104 Predicted transcriptional regulator [Transcription] 97.25
PRK1007296 putative transcriptional regulator; Provisional 96.88
pfam0172665 LexA_DNA_bind LexA DNA binding domain. This is the DNA 95.61
COG2522119 Predicted transcriptional regulator [General function p 94.72
pfam0152775 Transposase_8 Transposase. Transposase proteins are nec 94.59
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and related 94.28
PRK03975139 tfx putative transcriptional regulator; Provisional 93.9
PRK13756205 tetracycline repressor protein TetR; Provisional 93.23
pfam0421853 CENP-B_N CENP-B N-terminal DNA-binding domain. Centrome 93.17
pfam0522545 HTH_psq helix-turn-helix, Psq domain. This DNA-binding 91.79
pfam04814177 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus 91.65
COG2524294 Predicted transcriptional regulator, contains C-termina 90.62
PRK09480194 slmA nucleoid occlusion protein; Provisional 90.46
KOG0171176 consensus 96.77
PRK08099 411 nicotinamide-nucleotide adenylyltransferase; Provisiona 94.03
>COG2932 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK00215 LexA repressor; Validated Back     alignment and domain information
>PRK12423 LexA repressor; Provisional Back     alignment and domain information
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms] Back     alignment and domain information
>TIGR00498 lexA LexA repressor; InterPro: IPR006200 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes Back     alignment and domain information
>PHA00361 cI Repressor Back     alignment and domain information
>PRK10276 DNA polymerase V subunit UmuD; Provisional Back     alignment and domain information
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell Back     alignment and domain information
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families Back     alignment and domain information
>pfam00717 Peptidase_S24 Peptidase S24-like Back     alignment and domain information
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease; InterPro: IPR014124 Members of this protein family are predicted proteases that are encoded adjacent to the genes for a nickel-type superoxide dismutase (IPR014123 from INTERPRO) Back     alignment and domain information
>TIGR02227 sigpep_I_bact signal peptidase I; InterPro: IPR000223 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes Back     alignment and domain information
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3 Back     alignment and domain information
>TIGR02228 sigpep_I_arch signal peptidase I; InterPro: IPR001733 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes Back     alignment and domain information
>KOG1568 consensus Back     alignment and domain information
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion] Back     alignment and domain information
>PRK10861 lsignal peptidase I; Provisional Back     alignment and domain information
>KOG3342 consensus Back     alignment and domain information
>PRK09706 transcriptional repressor DicA; Reviewed 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
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional Back     alignment and domain information
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins Back     alignment and domain information
>COG1476 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed Back     alignment and domain information
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription] Back     alignment and domain information
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain Back     alignment and domain information
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [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
>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
>PRK08359 transcription factor; Validated Back     alignment and domain information
>PRK06424 transcription factor; Provisional Back     alignment and domain information
>PRK04140 hypothetical protein; Provisional Back     alignment and domain information
>COG1709 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG3655 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>COG4800 Predicted transcriptional regulator with an 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
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only] Back     alignment and domain information
>KOG3398 consensus Back     alignment and domain information
>COG1395 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional Back     alignment and domain information
>COG3423 Nlp Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional Back     alignment and domain information
>COG1396 HipB Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown] 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
>PHA00542 putative Cro-like protein Back     alignment and domain information
>COG3636 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>pfam08667 BetR BetR domain Back     alignment and domain information
>PRK10856 hypothetical protein; Provisional 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
>PRK09526 lacI lac repressor; Reviewed Back     alignment and domain information
>COG5499 Predicted transcription regulator containing HTH domain [Transcription] Back     alignment and domain information
>PRK02866 cyanate hydratase; Validated Back     alignment and domain information
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional Back     alignment and domain information
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins Back     alignment and domain information
>PRK09492 treR trehalose repressor; Provisional Back     alignment and domain information
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional Back     alignment and domain information
>pfam02001 DUF134 Protein of unknown function DUF134 Back     alignment and domain information
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional Back     alignment and domain information
>pfam00356 LacI Bacterial regulatory proteins, lacI family Back     alignment and domain information
>COG2944 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>PRK10072 putative transcriptional regulator; Provisional Back     alignment and domain information
>pfam01726 LexA_DNA_bind LexA DNA binding domain Back     alignment and domain information
>COG2522 Predicted transcriptional regulator [General function prediction only] Back     alignment and domain information
>pfam01527 Transposase_8 Transposase 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
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>PRK13756 tetracycline repressor protein TetR; Provisional Back     alignment and domain information
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain Back     alignment and domain information
>pfam05225 HTH_psq helix-turn-helix, Psq domain Back     alignment and domain information
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus Back     alignment and domain information
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription] Back     alignment and domain information
>PRK09480 slmA nucleoid occlusion protein; Provisional Back     alignment and domain information
>KOG0171 consensus Back     alignment and domain information
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional 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
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
3bdn_A236 Crystal Structure Of The Lambda Repressor Length = 9e-17
3k2z_A196 Crystal Structure Of A Lexa Protein From Thermotoga 6e-14
1jhh_A202 Lexa S119a Mutant Length = 202 6e-12
1jhf_A202 Lexa G85d Mutant Length = 202 2e-11
3jso_A202 Classic Protein With A New Twist: Crystal Structure 5e-11
1jhc_A137 Lexa S119a C-Terminal Tryptic Fragment Length = 137 6e-11
1umu_A116 Structure Determination Of Umud' By Mad Phasing Of 9e-10
1i4v_A115 Solution Structure Of The Umud' Homodimer Length = 1e-09
1ay9_A108 Wild-Type Umud' From E. Coli Length = 108 1e-09
1jhe_A135 Lexa L89p Q92w E152a K156a Mutant Length = 135 3e-09
1kca_A109 Crystal Structure Of The Lambda Repressor C-Termina 9e-11
1f39_A101 Crystal Structure Of The Lambda Repressor C-Termina 1e-10
2ho0_A133 Structure Of A Hyper-Cleavable Monomeric Fragment O 6e-10
2hnf_A133 Structure Of A Hyper-Cleavable Monomeric Fragment O 1e-08
1b0n_A111 Sinr ProteinSINI PROTEIN COMPLEX Length = 111 3e-04
>gi|183448279|pdb|3BDN|A Chain A, Crystal Structure Of The Lambda Repressor Length = 236 Back     alignment and structure
 Score = 91.4 bits (225), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 29/233 (12%), Positives = 71/233 (30%), Gaps = 19/233 (8%)

Query: 2   TSFSHKKI--WEAIDRMAE----RHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPST 55
              + +++     +  + E       L+   +A K G+  +                 + 
Sbjct: 5   KPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAAL 64

Query: 56  ESIFKIL-----AATNETICQLLDLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFP 110
             + KIL       +     ++ ++  +       + +    ++          +   F 
Sbjct: 65  --LAKILKVSVEEFSPSIAREIYEMYEAVSMQPSLRSEYEYPVFSHVQAGMFSPELRTFT 122

Query: 111 TGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDR 170
            G+    V   +  S       ++       T      P +  G +++++    V  GD 
Sbjct: 123 KGDAERWVSTTKKASDSAFWLEVEGNSMTAPT---GSKPSFPDGMLILVDPEQAVEPGDF 179

Query: 171 LLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARILWASQ 223
            + +    +   K LI      + L  LN  YP+          + +++ ASQ
Sbjct: 180 CIARLGGDEFTFKKLIR-GSGQVFLQPLNPQYPMIPCN-ESCSVVGKVI-ASQ 229


>gi|308198487|pdb|3K2Z|A Chain A, Crystal Structure Of A Lexa Protein From Thermotoga Maritima Length = 196 Back     alignment and structure
>gi|15988320|pdb|1JHH|A Chain A, Lexa S119a Mutant Length = 202 Back     alignment and structure
>gi|15988318|pdb|1JHF|A Chain A, Lexa G85d Mutant Length = 202 Back     alignment and structure
>gi|303324865|pdb|3JSO|A Chain A, Classic Protein With A New Twist: Crystal Structure Of A Lexa Repressor Dna Complex Length = 202 Back     alignment and structure
>gi|15988315|pdb|1JHC|A Chain A, Lexa S119a C-Terminal Tryptic Fragment Length = 137 Back     alignment and structure
>gi|1827863|pdb|1UMU|A Chain A, Structure Determination Of Umud' By Mad Phasing Of The Selenomethionyl Protein Length = 116 Back     alignment and structure
>gi|253722209|pdb|1I4V|A Chain A, Solution Structure Of The Umud' Homodimer Length = 115 Back     alignment and structure
>gi|2914397|pdb|1AY9|A Chain A, Wild-Type Umud' From E. Coli Length = 108 Back     alignment and structure
>gi|15988316|pdb|1JHE|A Chain A, Lexa L89p Q92w E152a K156a Mutant Length = 135 Back     alignment and structure
>gi|18158895|pdb|1KCA|A Chain A, Crystal Structure Of The Lambda Repressor C-Terminal Domain Octamer Length = 109 Back     alignment and structure
>gi|9955121|pdb|1F39|A Chain A, Crystal Structure Of The Lambda Repressor C-Terminal Domain Length = 101 Back     alignment and structure
>gi|116667752|pdb|2HO0|A Chain A, Structure Of A Hyper-Cleavable Monomeric Fragment Of Phage Lambda Repressor Containing The Cleavage Site Region Length = 133 Back     alignment and structure
>gi|116667750|pdb|2HNF|A Chain A, Structure Of A Hyper-Cleavable Monomeric Fragment Of Phage Lambda Repressor Containing The Cleavage Site Region Length = 133 Back     alignment and structure
gi|4389349|pdb|1B0N|A Chain A, Sinr ProteinSINI PROTEIN COMPLEX Length = 111 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
2fjr_A189 Repressor protein CI; genetic switch, regulation, coope 1e-05
3bdn_A236 Lambda repressor; repressor, allostery; HET: DNA; 3.91A 8e-04
3ivp_A126 Putative transposon-related DNA-binding protein; APC626 0.003
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A Length = 189 Back     alignment and structure
 Score = 45.1 bits (106), Expect = 1e-05
 Identities = 25/213 (11%), Positives = 55/213 (25%), Gaps = 41/213 (19%)

Query: 11  EAIDRMAERHNL-TPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETI 69
           + +DR+ E +       LA    +  +S +     G    +                ET 
Sbjct: 9   DVLDRICEAYGFSQKIQLANHFDIASSSLSNRYTRGAISYD---------FAAHCALETG 59

Query: 70  CQLLDLPFSDGRTTEKKEKEIPLLYFP--PSGSGGFFDSGVFPTGNKWNTVGVPEIRSPH 127
             L  L   +G       +                           ++ T  +       
Sbjct: 60  ANLQWLLTGEGEAFVNNRESSDAKRIEGFTLSEEILKSDKQLSVDAQFFTKPL------- 112

Query: 128 NGIYAIQTQDTRHKTQDTSMLPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLIS 187
                            T  + +  +G I  ++    ++ G  L+       I  + L  
Sbjct: 113 -----------------TDGMAIRSEGKIYFVDKQASLSDGLWLVDIKGAISI--RELTK 153

Query: 188 RRGRSIDLMSLNCCYPVDTVEMSDIEWIARILW 220
             GR + +      +      + DI+ + R++ 
Sbjct: 154 LPGRKLHVAGGKVPFE---CGIDDIKTLGRVVG 183


>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236 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

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
3bdn_A236 Lambda repressor; repressor, allostery; HET: DNA; 3.91A 99.97
1jhf_A202 LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {E 99.95
2fjr_A189 Repressor protein CI; genetic switch, regulation, coope 99.94
3k2z_A196 LEXA repressor; winged helix-turn-helix, SOS system, au 99.93
2hnf_A133 Repressor protein CI101-229DM-K192A; viral protein; 1.8 99.84
1kca_A109 Repressor protein CI; gene regulation, DNA-binding, lam 99.79
1umu_A116 UMUD'; induced mutagenesis, SOS mutagenesis, DNA repair 99.69
1b12_A 248 Signal peptidase I; serine proteinase, serine-dependant 97.62
1y9q_A192 Transcriptional regulator, HTH_3 family; transcriptiona 99.31
2bnm_A198 Epoxidase; oxidoreductase, cupin, HTH, cation-dependant 99.3
2ewt_A71 BLDD, putative DNA-binding protein; the DNA-binding dom 99.08
3op9_A114 PLI0006 protein; structural genomics, PSI-2, protein st 99.07
3b7h_A78 Prophage LP1 protein 11; structural genomics, PSI2, MCS 98.99
2ict_A94 Antitoxin HIGA; helix-turn-helix, structural genomics, 98.99
1b0n_A111 Protein (SINR protein); transcription regulator, antago 98.98
3ivp_A126 Putative transposon-related DNA-binding protein; APC626 98.98
3f52_A117 CLP gene regulator (CLGR); helix-turn-helix motif, tran 98.95
2kpj_A94 SOS-response transcriptional repressor, LEXA; NESG, GFT 98.95
1adr_A76 P22 C2 repressor; transcription regulation; NMR {Entero 98.93
3g7d_A443 PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic 98.93
3omt_A73 Uncharacterized protein; structural genomics, PSI-2, pr 98.92
3g5g_A99 Regulatory protein; transcriptional regulator, helix-tu 98.92
2wiu_B88 HTH-type transcriptional regulator HIPB; transferase tr 98.91
2b5a_A77 C.BCLI; helix-turn-helix motif, gene regulation; 1.54A 98.91
3mlf_A111 Transcriptional regulator; structural genomics, helix-t 98.91
1zug_A71 Phage 434 CRO protein; gene regulating protein, transcr 98.89
3bs3_A76 Putative DNA-binding protein; XRE-family, structural ge 98.88
1y7y_A74 C.AHDI; helix-turn-helix, DNA-binding protein, transcri 98.87
3f6w_A83 XRE-family like protein; helix-turn-helix, DNA binding 98.87
2jvl_A107 TRMBF1; coactivator, helix-turn-helix, Pro binding, tra 98.86
2r1j_L68 Repressor protein C2; protein-DNA complex, helix-turn-h 98.86
3clc_A82 Regulatory protein; protein-DNA complex, transcriptiona 98.86
1x57_A91 Endothelial differentiation-related factor 1; HMBF1alph 98.83
1r69_A69 Repressor protein CI; gene regulating protein; 2.00A {P 98.83
2l49_A99 C protein; P2 bacteriophage, P2 C, direct repeats, DNA- 98.82
3kz3_A80 Repressor protein CI; five helix bundle, DNA-binding, t 98.81
2p5t_A158 Putative transcriptional regulator PEZA; postsegregatio 98.8
3kxa_A141 NGO0477 protein, putative uncharacterized protein; NEW 98.78
2a6c_A83 Helix-turn-helix motif; putative transcriptional regula 98.78
1utx_A66 CYLR2; DNA-binding protein, transcriptional repressor, 98.76
1lmb_392 Protein (lambda repressor); protein-DNA complex, double 98.75
2ef8_A84 C.ECOT38IS, putative transcription factor; helix-turn-h 98.69
3cec_A104 Putative antidote protein of plasmid maintenance system 98.66
3eus_A86 DNA-binding protein; structural genomics, PSI2,MCSG, pr 98.64
2ofy_A86 Putative XRE-family transcriptional regulator; transcri 98.63
3fmy_A73 HTH-type transcriptional regulator MQSA (YGIT/B3021); h 98.49
2awi_A 317 PRGX; repressor, pheromone, DNA binding, regulatory dom 98.35
2o38_A120 Hypothetical protein; alpha-beta, helix-turn-helix, str 98.26
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; HTH- 98.21
2eby_A113 Putative HTH-type transcriptional regulator YBAQ; hypot 98.19
2qfc_A293 PLCR protein; TPR, HTH, transcription regulation; 2.60A 98.16
2wus_R112 RODZ, putative uncharacterized protein; structural prot 98.15
2ppx_A99 AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif 98.01
3fym_A130 Putative uncharacterized protein; HTH DNA binding, DNA 97.84
3bd1_A79 CRO protein; transcription factor, helix-turn-helix, pr 97.18
1dw9_A156 Cyanate lyase; cyanate degradation, structural genomics 97.01
1neq_A74 DNA-binding protein NER; NMR {Enterobacteria phage MU} 96.12
1uxc_A65 FRUR (1-57), fructose repressor; DNA-binding protein, L 92.41
3kjx_A 344 Transcriptional regulator, LACI family; LACL family, pr 92.38
1zs4_A83 Regulatory protein CII; helix-turn-helix, transcription 92.04
1rzs_A61 Antirepressor, regulatory protein CRO; helix-turn-helix 90.31
2auw_A170 Hypothetical protein NE0471; alpha-beta structure, stru 97.59
3nnr_A228 Transcriptional regulator, TETR family; TETR-family tra 95.61
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn-heli 95.1
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated reco 95.01
1zx4_A192 P1 PARB, plasmid partition PAR B protein, PARB; transla 94.98
2vke_A207 Tetracycline repressor protein class D; transcription, 94.91
2yve_A185 Transcriptional regulator; helix-turn-helix, TETR-famil 94.87
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, nati 94.77
2w48_A315 Sorbitol operon regulator; SORC, activator, repressor, 94.71
2opt_A234 Actii protein; helical protein, TETR family, APO-protei 94.57
1r71_A178 Transcriptional repressor protein KORB; INCP, plasmid p 94.34
2vpr_A207 Tetracycline resistance repressor protein; transcriptio 94.19
3cta_A230 Riboflavin kinase; structural genomics, transferase, PS 93.79
3fiw_A211 Putative TETR-family transcriptional regulator; TETR-fa 93.7
1j5y_A187 Transcriptional regulator, biotin repressor family; str 93.69
2eh3_A179 Transcriptional regulator; all alpha proteins, tetracyc 93.4
2fbq_A235 Probable transcriptional regulator; PA3006, APC5893, st 93.35
3frq_A195 Repressor protein MPHR(A); macrolide antibiotic. repres 93.3
3dpj_A194 Transcription regulator, TETR family; APC88616, silicib 93.04
1on2_A142 Transcriptional regulator MNTR; helix-turn-helix, DNA-b 93.02
3mky_B189 Protein SOPB; partition, F plasmid, centromere, DNA bin 92.94
2id3_A225 Putative transcriptional regulator; structural genomics 92.84
3bqy_A209 Putative TETR family transcriptional regulator; structu 92.75
2g7l_A243 TETR-family transcriptional regulator; APC6062, protein 92.72
3o60_A185 LIN0861 protein; PSI, MCSG, structural genomics, midwes 92.68
2o7t_A199 Transcriptional regulator; NP_600854.1, structural geno 92.66
2d6y_A202 Putative TETR family regulatory protein; helix-turn-hel 92.39
1u78_A141 TC3 transposase, transposable element TC3 transposase; 92.3
3jsj_A190 Putative TETR-family transcriptional regulator; NP_8213 92.08
3gzi_A218 Transcriptional regulator, TETR family; TETR family tra 92.02
2hxi_A241 Putative transcriptional regulator; structural genomics 92.0
2qwt_A196 Transcriptional regulator, TETR family; structural geno 91.73
2guh_A214 Putative TETR-family transcriptional regulator; helix-t 91.66
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein struct 91.66
1zk8_A183 Transcriptional regulator, TETR family; TETR member,tra 91.59
2dg8_A193 Putative TETR-family transcriptional regulatory protein 91.51
2wui_A210 MEXZ, transcriptional regulator; gene regulation, trans 91.49
1t33_A224 Putative transcriptional repressor (TETR/ACRR family); 91.46
3g7r_A221 Putative transcriptional regulator; TETR, all-helical, 91.35
3lhq_A220 Acrab operon repressor (TETR/ACRR family); structural g 91.29
2iu5_A195 DHAS, hypothetical protein YCEG; synthase, activator, T 91.27
2fq4_A192 Transcriptional regulator, TETR family; DNA-binding pro 91.24
2hyt_A197 TETR-family transcriptional regulator; structural genom 91.22
3kz9_A206 SMCR; transcriptional regulator, quorum S DNA-binding, 91.06
1ui5_A215 A-factor receptor homolog; helix-turn-helix, alpha-heli 91.02
2q24_A194 Putative TETR family transcriptional regulator; structu 90.98
3bjb_A207 Probable transcriptional regulator, TETR family protein 90.78
3on4_A191 Transcriptional regulator, TETR family; structural geno 90.78
3bni_A229 Putative TETR-family transcriptional regulator; structu 90.72
2hxo_A237 Putative TETR-family transcriptional regulator; TETR tr 90.6
3bru_A222 Regulatory protein, TETR family; structural genomics, A 90.59
1umq_A81 Photosynthetic apparatus regulatory protein; DNA-bindin 90.57
2gen_A197 Probable transcriptional regulator; APC6095, TETR famil 90.53
2f07_A197 YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A 90.5
3bqz_B194 HTH-type transcriptional regulator QACR; multidrug resi 90.47
1vi0_A206 Transcriptional regulator; structural genomics; HET: MS 90.42
2nx4_A194 Transcriptional regulator, TETR family protein; HTH DNA 90.41
2np5_A203 Transcriptional regulator; TETR family, structural geno 90.38
2zcx_A231 SCO7815, TETR-family transcriptional regulator; helix-t 90.36
1z05_A 429 Transcriptional regulator, ROK family; structural genom 90.36
3cwr_A208 Transcriptional regulator, TETR family; YP_425770.1, tr 90.29
1z6r_A 406 MLC protein; transcriptional repressor, ROK family prot 90.26
3mvp_A217 TETR/ACRR transcriptional regulator; PSI, MCSG, structu 90.22
3dew_A206 Transcriptional regulator, TETR family; structural geno 90.21
2wte_A244 CSA3; antiviral protein, viral resistance, winged helix 90.16
2x4h_A139 Hypothetical protein SSO2273; transcription; 2.30A {Sul 90.05
2rek_A199 Putative TETR-family transcriptional regulator; sulfur, 90.03
3ni7_A213 Bacterial regulatory proteins, TETR family; transcripti 90.01
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Back     alignment and structure
Probab=99.97  E-value=1.6e-31  Score=222.74  Aligned_cols=203  Identities=12%  Similarity=0.086  Sum_probs=145.9

Q ss_pred             CCCCCHHH------HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCC
Q ss_conf             97755899------999999999964999889999828998798899751578875577989999987321875210000
Q gi|254780444|r    1 MTSFSHKK------IWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAATNETICQLLD   74 (223)
Q Consensus         1 ~~~~~~~~------i~~~i~~l~~~~gls~~~lA~~~Gv~~~ti~~~~~~~~~g~~r~p~~~~l~kia~~~~v~~~~l~~   74 (223)
                      ++++|-++      +.+.++++|+++||||++||+++|++++||++|++|..     .|+.+.|.++|++++++++||..
T Consensus         4 ~~~~~~~~~~~~~rLk~l~~~~r~e~Glsq~elA~~~Gis~~tis~~e~G~~-----~~~~~~l~~ia~~l~v~~~~l~~   78 (236)
T 3bdn_A            4 KKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGIN-----ALNAYNAALLAKILKVSVEEFSP   78 (236)
T ss_dssp             SCCCCSHHHHHHHHHHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTTTS-----CCCHHHHHHTTTTTTSCGGGTCH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCC-----HHHHHHHHHHHHHCEEEEEHHCC
T ss_conf             8989999999999999999999998399999999997979999988872852-----46799999752202785121103


Q ss_pred             CCCCCCCCC---------CCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             111124445---------44221220243101134522211125444640356437211354542003685599996283
Q gi|254780444|r   75 LPFSDGRTT---------EKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDT  145 (223)
Q Consensus        75 ~~~~~~~~~---------~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GD  145 (223)
                      .........         .......++....+++......          +.................+.++++++|.||
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ag~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~~l~v~Gd  148 (236)
T 3bdn_A           79 SIAREIYEMYEAVSMQPSLRSEYEYPVFSHVQAGMFSPEL----------RTFTKGDAERWVSTTKKASDSAFWLEVEGN  148 (236)
T ss_dssp             HHHHHHHHHHHHHHCCCCSSCSCCCCCCCSSCCCCTTTTC----------CCCSSCCCCCCCCCSCCCSSSCEEEECCSS
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCC----------CCCCCCCCEEEEEECCCCCCCEEEEEEECC
T ss_conf             2232322222212235543332112431353157752245----------553234321344202479877399999622


Q ss_pred             CC------CCCCCCCCEEEEECCCCCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHHEEEEEEEE
Q ss_conf             32------421487868999368974058889999717968999999977987999968589887585478659997799
Q gi|254780444|r  146 SM------LPLYRKGDILILNSAIQVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSDIEWIARIL  219 (223)
Q Consensus       146 SM------~P~i~~Gd~vlVd~~~~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~i~iigrVv  219 (223)
                      ||      +|.|++||+++||+..+..+|++||++..+++++|||+++. ++.+.|+|+||+||++.+. ++++||||||
T Consensus       149 sM~~~~~~ep~i~~Gd~v~vd~~~~~~~~~~v~v~~~~~~~~iKrl~~~-~~~~~L~s~N~~y~~~~~~-~~~~IiG~Vv  226 (236)
T 3bdn_A          149 SMTAPTGSKPSFPDGMLILVDPEQAVEPGDFCIARLGGDEFTFKKLIRG-SGQVFLQPLNPQYPMIPCN-ESCSVVGKVI  226 (236)
T ss_dssp             SSCCCSSCSSCCCSSCEEEECCSSCCCTTSEEEEESTTTCCCCEEEECC-SSSCEEECSSTTSCCBC---CCCEEEEEEE
T ss_pred             CCCCCCCCCCEEECCEEEEEECCCCCCCCCEEEEEECCCEEEEEEEEEE-CCEEEEEECCCCCCCEECC-CCCEEEEEEE
T ss_conf             0577778898886880687614543213878999986999999999997-9989999899998978659-9969999999


Q ss_pred             E
Q ss_conf             8
Q gi|254780444|r  220 W  220 (223)
Q Consensus       220 w  220 (223)
                      +
T Consensus       227 ~  227 (236)
T 3bdn_A          227 A  227 (236)
T ss_dssp             E
T ss_pred             E
T ss_conf             8



>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
>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A Back     alignment and structure
>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima} Back     alignment and structure
>2hnf_A Repressor protein CI101-229DM-K192A; viral protein; 1.80A {Escherichia coli} PDB: 2ho0_A 1f39_A Back     alignment and structure
>1kca_A Repressor protein CI; gene regulation, DNA-binding, lambda repressor, protein oligomerization, DNA-looping; 2.91A {Enterobacteria phage lambda} SCOP: b.87.1.1 Back     alignment and structure
>1umu_A UMUD'; induced mutagenesis, SOS mutagenesis, DNA repair, beta- lactamase cleavage reaction, LEXA repressor, lambda CI; 2.50A {Escherichia coli} SCOP: b.87.1.1 PDB: 1i4v_A 1ay9_A Back     alignment and structure
>1b12_A Signal peptidase I; serine proteinase, serine-dependant hydrolase, signal peptide processing, protein translocation; HET: 1PN; 1.95A {Escherichia coli BL21} SCOP: b.87.1.2 PDB: 1t7d_A* 3iiq_A* 1kn9_A* 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
>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
>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
>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
>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
>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
>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
>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
>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
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 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
>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
>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A 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
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 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
>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
>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
>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
>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
>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} 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
>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
>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
>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
>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
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli} Back     alignment and structure
>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovarisraelensis atcc 35646} 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
>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp} 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
>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
>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
>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
>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
>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
>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei} Back     alignment and structure
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_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
>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
>2vke_A Tetracycline repressor protein class D; transcription, metal-binding, helix-turn-helix, transcription regulator, transcription regulation; HET: TAC; 1.62A {Escherichia coli} SCOP: a.4.1.9 a.121.1.1 PDB: 1bjy_A* 1bj0_A 1du7_A* 1ork_A* 2fj1_A* 1bjz_A* 2o7o_A* 2tct_A* 2trt_A* 1qpi_A* 1a6i_A 2vkv_A* 3fk7_A* 3fk6_A* 2ns7_A 2ns8_A Back     alignment and structure
>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A* Back     alignment and structure
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} 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
>2opt_A Actii protein; helical protein, TETR family, APO-protein, transcriptional repressor; 2.05A {Streptomyces coelicolor} PDB: 3b6a_A* 3b6c_A* 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
>2vpr_A Tetracycline resistance repressor protein; transcription, metal-binding, antibiotic resistance, transcription regulator; HET: TDC; 2.49A {Pasteurella multocida} Back     alignment and structure
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2 Back     alignment and structure
>3fiw_A Putative TETR-family transcriptional regulator; TETR-family transcriptional regulator streptomyces, structural genomics, PSI-2; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>1j5y_A Transcriptional regulator, biotin repressor family; structural genomics, TM1602, JCSG, conserved hypothetical protein, PSI; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1 Back     alignment and structure
>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin repressor-like, C-terminal domain, homeodomain-like; 1.55A {Aquifex aeolicus VF5} Back     alignment and structure
>2fbq_A Probable transcriptional regulator; PA3006, APC5893, structural genomics, PSI, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>3frq_A Repressor protein MPHR(A); macrolide antibiotic. repressor, biosensor, erythromycin, STRPTOMYCES, natural products, biosynthesis, DNA-binding; HET: ERY; 1.76A {Escherichia coli} PDB: 3g56_A Back     alignment and structure
>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi} Back     alignment and structure
>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 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
>2id3_A Putative transcriptional regulator; structural genomics, PSI-2, prote structure initiative; 1.70A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>3bqy_A Putative TETR family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.95A {Streptomyces coelicolor A3} Back     alignment and structure
>2g7l_A TETR-family transcriptional regulator; APC6062, protein structure initiative, PSI, midwest center for structural genomics, MCSG; 2.10A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>3o60_A LIN0861 protein; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative, unknown function; 2.80A {Listeria innocua} Back     alignment and structure
>2o7t_A Transcriptional regulator; NP_600854.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor A3} SCOP: a.4.1.9 a.121.1.1 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
>3jsj_A Putative TETR-family transcriptional regulator; NP_821317.1, putative transcriptional regulator, structural genomics; 2.10A {Streptomyces avermitilis ma-4680} Back     alignment and structure
>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4} Back     alignment and structure
>2hxi_A Putative transcriptional regulator; structural genomics, APC6293, TETR family, PSI-2, protein structure initiative; 1.70A {Streptomyces coelicolor A3} Back     alignment and structure
>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1} Back     alignment and structure
>2guh_A Putative TETR-family transcriptional regulator; helix-turn-helix, TETR fold, structural genomics, PSI, protein structure initiative; HET: MSE; 1.52A {Rhodococcus SP} 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
>1zk8_A Transcriptional regulator, TETR family; TETR member,transcriptional regulator, structural genomics, PSI, protein structure initiative; 2.15A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2dg8_A Putative TETR-family transcriptional regulatory protein; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor A3} Back     alignment and structure
>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription regulation, TETR, DNA-binding transcription; 2.90A {Pseudomonas aeruginosa} Back     alignment and structure
>1t33_A Putative transcriptional repressor (TETR/ACRR family); structural genomics, TETR/CCRR family, helix turn helix DNA binding domain; 2.20A {Salmonella typhimurium LT2} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>3g7r_A Putative transcriptional regulator; TETR, all-helical, structural genomics, PSI-2, protein structure initiative; 1.38A {Streptomyces coelicolor A3} Back     alignment and structure
>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A Back     alignment and structure
>2iu5_A DHAS, hypothetical protein YCEG; synthase, activator, TETR family, dihydroxyacetone; 1.6A {Lactococcus lactis subsp} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2hyt_A TETR-family transcriptional regulator; structural genomics, center for structural genomics, JCSG, protein structure INI PSI-2; HET: MSE; 1.64A {Pectobacterium atrosepticum} Back     alignment and structure
>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A Back     alignment and structure
>1ui5_A A-factor receptor homolog; helix-turn-helix, alpha-helix-bundle, antibiotic; 2.40A {Streptomyces coelicolor A3} SCOP: a.4.1.9 a.121.1.1 PDB: 1ui6_A Back     alignment and structure
>2q24_A Putative TETR family transcriptional regulator; structural genomics, PSI, protein structure initiative; 1.80A {Streptomyces coelicolor A3} Back     alignment and structure
>3bjb_A Probable transcriptional regulator, TETR family protein; APC7331, rhodococcus SP. RHA1, structural genomics, PSI-2, protein structure initiative; 2.50A {Rhodococcus SP} Back     alignment and structure
>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp} Back     alignment and structure
>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281, TETR transcriptional regulator, PSI-2; HET: PG4; 2.30A {Streptomyces coelicolor A3} Back     alignment and structure
>2hxo_A Putative TETR-family transcriptional regulator; TETR transcriptional regulator, structural genomics, PSI-2; 2.40A {Streptomyces coelicolor A3} Back     alignment and structure
>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structure initiative; 2.30A {Rhodobacter sphaeroides 2} Back     alignment and structure
>2gen_A Probable transcriptional regulator; APC6095, TETR family, structural genomics, PSI, protein structure initiative; 1.70A {Pseudomonas aeruginosa PAO1} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp} Back     alignment and structure
>3bqz_B HTH-type transcriptional regulator QACR; multidrug resistance, TETR, malachite green, DNA- binding, plasmid, repressor; HET: MGR; 2.17A {Staphylococcus aureus} PDB: 3br1_B* 3br3_B* 1rkw_B* 1jt0_A* 1jty_B* 1jum_B* 1jup_B* 1jtx_B* 1jus_B* 2dtz_B 2gby_B* 2hq5_B 3br2_B* 3br5_B* 1qvt_B* 1qvu_B* 3br0_B* 3br6_B* 1jt6_B* 1rpw_A* ... Back     alignment and structure
>1vi0_A Transcriptional regulator; structural genomics; HET: MSE DCC; 1.65A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2nx4_A Transcriptional regulator, TETR family protein; HTH DNA binding motif, structural genomics, PSI-2, protein structure initiative; 1.70A {Rhodococcus SP} Back     alignment and structure
>2np5_A Transcriptional regulator; TETR family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE LMT NDS; 1.80A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1 Back     alignment and structure
>2zcx_A SCO7815, TETR-family transcriptional regulator; helix-turn-helix, DNA-binding, transcription regulation; 2.22A {Streptomyces coelicolor} Back     alignment and structure
>1z05_A Transcriptional regulator, ROK family; structural genomics, PSI, protein structure initiative; 2.00A {Vibrio cholerae o1 biovar eltor str} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 Back     alignment and structure
>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170} Back     alignment and structure
>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding protein, helix-turn-helix, phosphotransferase system, metalloprotein; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A Back     alignment and structure
>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans} Back     alignment and structure
>3dew_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: MSE; 1.75A {Geobacter sulfurreducens} Back     alignment and structure
>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus} Back     alignment and structure
>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus} Back     alignment and structure
>2rek_A Putative TETR-family transcriptional regulator; sulfur, SAD, structural genomics, PSI-2, protein structure initiative; 1.86A {Streptomyces coelicolor A3} Back     alignment and structure
>3ni7_A Bacterial regulatory proteins, TETR family; transcriptional regulator, structural genomics, PSI-2, structure initiative; HET: MSE; 2.78A {Nitrosomonas europaea} 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 223 bacteriophage repressor protein C1 [Candidatus Liberiba
d2b5aa177 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus c 0.004
>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Length = 77 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]
 Score = 35.2 bits (81), Expect = 0.004
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 6  HKKIWEAIDRMAERHNLTPSGLARKAGLDPTSFNKSKRFGIEGRNRWPSTESIFKILAAT 65
           +K    + ++  +  ++   LA  AGL  T  ++     +E  +R  S  +I KI AA 
Sbjct: 8  KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISE-----VERGDRNISLINIHKICAAL 62

Query: 66 NETICQLLD 74
          +        
Sbjct: 63 DIPASTFFR 71


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

IdentityAlignment graphLength Definition Probability
Target223 bacteriophage repressor protein C1 [Candidatus Liberiba
d1jhfa2126 LexA C-terminal domain {Escherichia coli [TaxId: 562]} 99.8
d1f39a_101 lambda repressor C-terminal domain {Bacteriophage lambd 99.8
d1umua_105 UmuD' {Escherichia coli [TaxId: 562]} 99.66
d1b12a_ 247 Type 1 signal peptidase {Escherichia coli [TaxId: 562]} 97.69
d2b5aa177 Regulatory protein C.BclI {Bacillus caldolyticus [TaxId 98.91
d1y9qa179 Probable transcriptional regulator VC1968, N-terminal d 98.91
d2croa_65 cro 434 {Bacteriophage 434 [TaxId: 10712]} 98.9
d2r1jl166 P22 C2 repressor, DNA-binding domain {Salmonella bacter 98.89
d1y7ya169 Restriction-modification controller protein C.AhdI {Aer 98.89
d1b0na268 SinR repressor, DNA-binding domain {Bacillus subtilis [ 98.88
d1x57a178 Endothelial differentiation-related factor 1, EDF1 {Hum 98.82
d2o38a189 Hypothetical protein RPA3824 {Rhodopseudomonas palustri 98.82
d1lmb3_87 lambda C1 repressor, DNA-binding domain {Bacteriophage 98.78
d1r69a_63 434 C1 repressor, DNA-binding domain {Bacteriophage 434 98.78
d1utxa_66 Putative transcription regulator CylR2 {Enterococcus fa 98.78
d2a6ca169 HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 98.77
d2icta187 Antitoxin HigA {Escherichia coli [TaxId: 562]} 98.74
d2ofya182 Putative transcriptional regulator RHA1_ro04071 {Rhodoc 98.63
d2ppxa162 Uncharacterized protein Atu1735 {Agrobacterium tumefaci 98.07
d2bnma171 Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal 95.08
d1nera_74 Ner {Bacteriophage mu [TaxId: 10677]} 94.74
d1dwka186 Cyanase N-terminal domain {Escherichia coli [TaxId: 562 94.17
d1efaa159 Lac repressor (LacR), N-terminal domain {Escherichia co 90.82
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Escherich 90.67
d2hsga157 Glucose-resistance amylase regulator CcpA, N-terminal d 90.64
d1e3oc275 Oct-1 {Human (Homo sapiens) [TaxId: 9606]} 90.47
d1qpza157 Purine repressor (PurR), N-terminal domain {Escherichia 90.08
d2auwa167 Hypothetical protein NE0471 C-terminal domain {Nitrosom 97.62
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 95.74
d1ic8a294 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo s 95.1
d1v7ba174 Transcriptional regulator Cgl2612 {Corynebacterium glut 94.39
d1hlva166 DNA-binding domain of centromere binding protein B (CEN 94.16
d1j5ya165 Putative transcriptional regulator TM1602, N-terminal d 93.81
d1r71a_114 Transcriptional repressor protein KorB DNA-binding doma 93.74
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium glutam 93.59
d1zk8a172 Transcriptional regulator BC5000 {Bacillus cereus [TaxI 93.46
d1vz0a193 Putative partitioning protein ParB/Spo0J {Thermus therm 93.24
d2np5a169 Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. 93.08
d1jhfa171 LexA repressor, N-terminal DNA-binding domain {Escheric 92.82
d2fx0a173 Hemolysin II regulatory protein, HlyIIR {Bacillus cereu 92.63
d2fbqa179 Transcriptional regulator PsrA {Pseudomonas aeruginosa 92.52
d2g7sa174 Putative transcriptional regulator Atu0279 {Agrobacteri 92.3
d2g7la168 Putative transcriptional regulator SCO7704 {Streptomyce 91.95
d2g7ga165 Putative transcriptional regulator Rha04620 {Rhodococcu 91.7
d2fq4a169 Transcriptional regulator BC3163 {Bacillus cereus [TaxI 91.63
d3c07a175 Putative transcriptional regulator SCO4850 {Streptomyce 91.48
d2o7ta178 Transcriptional regulator Cgl1640/Cg1846 {Corynebacteri 91.41
d2iu5a171 Transcriptional activator DhaS {Lactococcus lactis [Tax 91.23
d2ev0a161 Manganese transport regulator MntR {Bacillus subtilis [ 91.07
d2id3a168 Putative transcriptional regulator SCO5951 {Streptomyce 91.05
d2gfna177 Probable transcriptional regulator RHA1_ro04631 {Rhodoc 91.0
d2oi8a179 Putative regulatory protein Sco4313 {Streptomyces coeli 90.87
d1pb6a172 Hypothetical transcriptional regulator YcdC {Escherichi 90.66
d2d6ya168 Putative regulator SCO4008 {Streptomyces coelicolor [Ta 90.63
d1jt6a171 Multidrug binding protein QacR {Staphylococcus aureus [ 90.59
d1z0xa168 Transcriptional regulator EF0787 {Enterococcus faecalis 90.56
d1t56a173 Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773 90.49
d2hkua170 Putative transcriptional regulator RHA1_ro03468 {Rhodoc 90.25
d1ui5a171 A-factor receptor homolog CprB {Streptomyces coelicolor 90.2
d1t33a188 Putative transcriptional repressor YbiH {Salmonella typ 90.13
>d1jhfa2 b.87.1.1 (A:73-198) LexA C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All beta proteins
fold: LexA/Signal peptidase
superfamily: LexA/Signal peptidase
family: LexA-related
domain: LexA C-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=99.80  E-value=3.9e-19  Score=141.05  Aligned_cols=118  Identities=14%  Similarity=0.152  Sum_probs=91.7

Q ss_pred             CCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCC-CCCCCEEEEECCCCCCC
Q ss_conf             22024310113452221112544464035643721135454200368559999628332421-48786899936897405
Q gi|254780444|r   89 EIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLPL-YRKGDILILNSAIQVNC  167 (223)
Q Consensus        89 ~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~P~-i~~Gd~vlVd~~~~~~~  167 (223)
                      .+|+++..+||......      ....+.+.++...       ..++++|+++|+||||+|+ |++||+|+|+++.++.+
T Consensus         3 ~IPv~g~v~AG~p~~a~------e~~e~~~~~~~~~-------~~~~~~f~lrV~GdSM~~~~i~~gd~viv~~~~~~~~   69 (126)
T d1jhfa2           3 GLPLVGRVAADEPLLAQ------QHIEGHYQVDPSL-------FKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRN   69 (126)
T ss_dssp             SEEEECCCCTTSCTTCG------GGEEEEECBCGGG-------SSSCCCEEEECCSSTTGGGTCCTTCEEEEEECSCCCT
T ss_pred             CCCEEEEECCCCCCHHH------CCCCCEEECCHHH-------CCCCCEEEEEECCCCCCCCCCCCCEEEEEECCCCCCC
T ss_conf             89888783698988002------0333248456899-------3888669999948766674147997999713640339


Q ss_pred             CCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECH--HHEEEEEEEEEE
Q ss_conf             888999971796899999997798799996858988758547--865999779985
Q gi|254780444|r  168 GDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEM--SDIEWIARILWA  221 (223)
Q Consensus       168 g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~--~~i~iigrVvw~  221 (223)
                      |++|++.. +|++++||+++. ++.++|.|+||+|+|+.++.  ++++|||||+.+
T Consensus        70 G~ivv~~~-~ge~~vKrl~~~-~~~~~L~s~N~~y~pi~~~~~~~~~~IiG~Vv~v  123 (126)
T d1jhfa2          70 GQVVVARI-DDEVTVKRLKKQ-GNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGV  123 (126)
T ss_dssp             TSEEEEEE-TTEEEEEEEEEE-TTEEEEECSSTTCCCEEEETTTSCEEEEEEEEEE
T ss_pred             CCEEEEEE-CCEEEEEEEEEC-CCEEEEECCCCCCCCEECCCCCCCEEEEEEEEEE
T ss_conf             98999999-999999999982-9999996478679976816888958999999999



>d1f39a_ b.87.1.1 (A:) lambda repressor C-terminal domain {Bacteriophage lambda [TaxId: 10710]} Back     information, alignment and structure