Citrus Sinensis ID: 036324

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-
MPHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
ccHHHHHHcccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHccccccHHHHHHHHHHHHHHHc
ccHHHHHHccccHHHHHHHcccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHc
mphlsrsiigsdiecvNQLRMDKRTFELLCGLLRingglkadgtVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
mphlsrsiigsdiecvNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
MPHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
*******IIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI**
*PHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
MPHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
MPHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MPHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query91
147779878 579 hypothetical protein VITISV_027369 [Viti 0.978 0.153 0.573 2e-21
413950101 445 hypothetical protein ZEAMMB73_878123 [Ze 1.0 0.204 0.516 6e-18
307135889 623 retrotransposon protein [Cucumis melo su 0.890 0.130 0.530 1e-17
147841225185 hypothetical protein VITISV_032219 [Viti 0.813 0.4 0.608 1e-17
413941984 288 hypothetical protein ZEAMMB73_204913 [Ze 1.0 0.315 0.516 2e-17
147769233 568 hypothetical protein VITISV_010914 [Viti 0.835 0.133 0.526 1e-14
359481135 261 PREDICTED: uncharacterized protein LOC10 0.835 0.291 0.539 2e-14
356561128 306 PREDICTED: uncharacterized protein LOC10 0.901 0.267 0.475 4e-14
356577175 507 PREDICTED: uncharacterized protein LOC10 0.967 0.173 0.465 5e-14
297608688 705 Os08g0459400 [Oryza sativa Japonica Grou 0.879 0.113 0.512 9e-14
>gi|147779878|emb|CAN65842.1| hypothetical protein VITISV_027369 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  106 bits (264), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/89 (57%), Positives = 66/89 (74%)

Query: 3   HLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHV 62
           +L+R I GSD+ C+ QLRMD+ TF  LC +LR  G LK    + +EE + +FLHILAHHV
Sbjct: 56  NLNRLIYGSDVACMEQLRMDRHTFTTLCSMLRTIGKLKDSKYIDVEEMVALFLHILAHHV 115

Query: 63  KSRTIHSRFLRSRETISRYFNLVLNAILQ 91
           K+R I  RFLRS ETISR+FN VLNA+++
Sbjct: 116 KNRVIKFRFLRSGETISRHFNAVLNAVIR 144

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|413950101|gb|AFW82750.1| hypothetical protein ZEAMMB73_878123 [Zea mays] Back     alignment and taxonomy information
>gi|307135889|gb|ADN33754.1| retrotransposon protein [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|147841225|emb|CAN62415.1| hypothetical protein VITISV_032219 [Vitis vinifera] Back     alignment and taxonomy information
>gi|413941984|gb|AFW74633.1| hypothetical protein ZEAMMB73_204913 [Zea mays] Back     alignment and taxonomy information
>gi|147769233|emb|CAN60760.1| hypothetical protein VITISV_010914 [Vitis vinifera] Back     alignment and taxonomy information
>gi|359481135|ref|XP_003632575.1| PREDICTED: uncharacterized protein LOC100852451 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356561128|ref|XP_003548837.1| PREDICTED: uncharacterized protein LOC100801437 [Glycine max] Back     alignment and taxonomy information
>gi|356577175|ref|XP_003556703.1| PREDICTED: uncharacterized protein LOC100780651 [Glycine max] Back     alignment and taxonomy information
>gi|297608688|ref|NP_001061974.2| Os08g0459400 [Oryza sativa Japonica Group] gi|255678502|dbj|BAF23888.2| Os08g0459400 [Oryza sativa Japonica Group] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query91
TAIR|locus:2165775 374 AT5G41980 [Arabidopsis thalian 0.890 0.216 0.432 8.6e-13
TAIR|locus:504956234 324 AT1G43722 "AT1G43722" [Arabido 0.813 0.228 0.405 3.3e-08
TAIR|locus:2184226 296 AT5G28730 "AT5G28730" [Arabido 0.945 0.290 0.325 2.6e-07
TAIR|locus:2165775 AT5G41980 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 175 (66.7 bits), Expect = 8.6e-13, P = 8.6e-13
 Identities = 35/81 (43%), Positives = 50/81 (61%)

Query:    10 GSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHS 69
             G + +C    RMDK  F  LC LL+  G L+    + IE QL +FL I+ H++++R +  
Sbjct:    37 GPNEQCFENFRMDKPVFYKLCDLLQTRGLLRHTNRIKIEAQLAIFLFIIGHNLRTRAVQE 96

Query:    70 RFLRSRETISRYFNLVLNAIL 90
              F  S ETISR+FN VLNA++
Sbjct:    97 LFCYSGETISRHFNNVLNAVI 117
GO:0005634 "nucleus" evidence=ISM
GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA
TAIR|locus:504956234 AT1G43722 "AT1G43722" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2184226 AT5G28730 "AT5G28730" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00001430001
SubName- Full=Chromosome undetermined scaffold_116, whole genome shotgun sequence; (524 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 91
PF1361353 HTH_Tnp_4: Helix-turn-helix of DDE superfamily end 98.92
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 97.27
PF1211682 SpoIIID: Stage III sporulation protein D; InterPro 96.5
TIGR03697193 NtcA_cyano global nitrogen regulator NtcA, cyanoba 96.35
COG3415138 Transposase and inactivated derivatives [DNA repli 96.34
PRK10402226 DNA-binding transcriptional activator YeiL; Provis 96.3
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 96.22
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 96.07
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 95.93
cd0657190 Bac_DnaA_C C-terminal domain of bacterial DnaA pro 95.92
PRK11753211 DNA-binding transcriptional dual regulator Crp; Pr 95.87
PRK11161235 fumarate/nitrate reduction transcriptional regulat 95.77
PRK09391230 fixK transcriptional regulator FixK; Provisional 95.72
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 95.48
PF0829970 Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli 95.36
PRK09392236 ftrB transcriptional activator FtrB; Provisional 95.31
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR- 95.27
smart00351125 PAX Paired Box domain. 95.15
cd00131128 PAX Paired Box domain 95.06
PRK06030124 hypothetical protein; Provisional 94.82
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 94.71
TIGR0253188 yecD_yerC TrpR-related protein YerC/YecD. This mod 94.52
PRK04217110 hypothetical protein; Provisional 94.41
PF0522545 HTH_psq: helix-turn-helix, Psq domain; InterPro: I 94.1
PRK13918202 CRP/FNR family transcriptional regulator; Provisio 94.06
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 93.47
PF1351852 HTH_28: Helix-turn-helix domain 93.31
cd0009267 HTH_CRP helix_turn_helix, cAMP Regulatory protein 93.3
PF1373055 HTH_36: Helix-turn-helix domain 92.77
KOG4585 326 consensus Predicted transposase [Replication, reco 92.73
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 92.68
PF1284061 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_ 92.6
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 92.55
TIGR0132194 TrpR trp operon repressor, proteobacterial. This m 92.5
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 92.34
PF0032532 Crp: Bacterial regulatory proteins, crp family; In 92.33
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 92.33
PRK09639166 RNA polymerase sigma factor SigX; Provisional 92.04
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 91.99
PF1354576 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 91.88
PRK00149450 dnaA chromosomal replication initiation protein; R 91.81
PF13551112 HTH_29: Winged helix-turn helix 91.51
PF0137187 Trp_repressor: Trp repressor protein; InterPro: IP 91.25
PF0827955 HTH_11: HTH domain; InterPro: IPR013196 Winged hel 91.16
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 90.99
PRK14088440 dnaA chromosomal replication initiation protein; P 90.94
PRK09413121 IS2 repressor TnpA; Reviewed 90.62
PRK14086617 dnaA chromosomal replication initiation protein; P 90.42
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 90.36
PF1334075 DUF4096: Putative transposase of IS4/5 family (DUF 90.34
PF0012660 HTH_1: Bacterial regulatory helix-turn-helix prote 89.95
PF01710119 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr 89.72
PRK00118104 putative DNA-binding protein; Validated 89.38
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 89.35
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 88.97
PRK15320251 transcriptional activator SprB; Provisional 88.92
PRK15411207 rcsA colanic acid capsular biosynthesis activation 88.54
smart0034284 HTH_ARAC helix_turn_helix, arabinose operon contro 88.37
TIGR00721137 tfx DNA-binding protein, Tfx family. Tfx from Meth 88.15
PF0132560 Fe_dep_repress: Iron dependent repressor, N-termin 87.92
PRK10840216 transcriptional regulator RcsB; Provisional 87.89
COG277165 CsgD DNA-binding HTH domain-containing proteins [T 87.83
PF1280262 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP 87.68
COG2197211 CitB Response regulator containing a CheY-like rec 87.58
PRK0138199 Trp operon repressor; Provisional 87.52
PRK09483217 response regulator; Provisional 87.5
PRK14087450 dnaA chromosomal replication initiation protein; P 87.46
PF0035646 LacI: Bacterial regulatory proteins, lacI family; 87.16
PHA00738108 putative HTH transcription regulator 87.07
TIGR02392270 rpoH_proteo alternative sigma factor RpoH. A sigma 86.94
PRK06930170 positive control sigma-like factor; Validated 86.78
TIGR0284480 spore_III_D sporulation transcriptional regulator 86.55
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 86.43
TIGR02393238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 86.18
smart0034691 HTH_ICLR helix_turn_helix isocitrate lyase regulat 86.1
PRK09492 315 treR trehalose repressor; Provisional 86.04
PRK11475207 DNA-binding transcriptional activator BglJ; Provis 85.85
PRK12524196 RNA polymerase sigma factor; Provisional 85.75
PRK12683 309 transcriptional regulator CysB-like protein; Revie 85.32
PRK09047161 RNA polymerase factor sigma-70; Validated 85.24
PRK10141117 DNA-binding transcriptional repressor ArsR; Provis 85.04
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 84.87
PRK12422445 chromosomal replication initiation protein; Provis 84.77
smart0076060 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix 84.65
PRK10651216 transcriptional regulator NarL; Provisional 84.49
PRK12679 316 cbl transcriptional regulator Cbl; Reviewed 84.38
PRK08301234 sporulation sigma factor SigE; Reviewed 84.35
PF13551112 HTH_29: Winged helix-turn helix 84.33
smart0041866 HTH_ARSR helix_turn_helix, Arsenical Resistance Op 84.29
PRK12514179 RNA polymerase sigma factor; Provisional 84.04
smart0034560 HTH_GNTR helix_turn_helix gluconate operon transcr 84.01
PF0104759 MarR: MarR family; InterPro: IPR000835 The MarR-ty 83.98
PRK03975141 tfx putative transcriptional regulator; Provisiona 83.93
PF0220936 VHP: Villin headpiece domain; InterPro: IPR003128 83.6
PRK15201198 fimbriae regulatory protein FimW; Provisional 83.53
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 83.13
PRK05911257 RNA polymerase sigma factor sigma-28; Reviewed 83.11
PRK12519194 RNA polymerase sigma factor; Provisional 82.98
TIGR02980227 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G 82.69
TIGR02835234 spore_sigmaE RNA polymerase sigma-E factor. Member 82.6
smart0015336 VHP Villin headpiece domain. 82.57
PRK05572252 sporulation sigma factor SigF; Validated 82.51
TIGR02885231 spore_sigF RNA polymerase sigma-F factor. Members 82.41
cd0737766 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi 82.24
smart0041948 HTH_CRP helix_turn_helix, cAMP Regulatory protein. 82.23
PRK13719217 conjugal transfer transcriptional regulator TraJ; 81.98
PRK10403215 transcriptional regulator NarP; Provisional 81.94
PHA0054282 putative Cro-like protein 81.61
PRK08583257 RNA polymerase sigma factor SigB; Validated 81.48
PHA0067578 hypothetical protein 81.24
PF01710119 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr 81.23
TIGR02941255 Sigma_B RNA polymerase sigma-B factor. This sigma 81.17
TIGR0161095 phage_O_Nterm phage replication protein O, N-termi 81.01
PRK06596284 RNA polymerase factor sigma-32; Reviewed 80.98
COG0593408 DnaA ATPase involved in DNA replication initiation 80.83
PF05732165 RepL: Firmicute plasmid replication protein (RepL) 80.79
PRK12682 309 transcriptional regulator CysB-like protein; Revie 80.78
TIGR03541232 reg_near_HchA LuxR family transcriptional regulato 80.64
PRK10360196 DNA-binding transcriptional activator UhpA; Provis 80.61
TIGR02405 311 trehalos_R_Ecol trehalose operon repressor, proteo 80.56
PRK07500289 rpoH2 RNA polymerase factor sigma-32; Reviewed 80.51
TIGR02850254 spore_sigG RNA polymerase sigma-G factor. Members 80.42
TIGR02997298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 80.27
TIGR0387973 near_KaiC_dom probable regulatory domain. This mod 80.16
PRK12537182 RNA polymerase sigma factor; Provisional 80.16
PF1330964 HTH_22: HTH domain 80.07
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease Back     alignment and domain information 
Probab=98.92  E-value=2.8e-09  Score=62.00  Aligned_cols=47  Identities=28%  Similarity=0.365  Sum_probs=44.7

Q ss_pred             CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324           44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL   90 (91)
Q Consensus        44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~   90 (91)
                      ..+.++|+.+.|..+.+|.++.+++.+||.|.+||||+|+++++.+.
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~   48 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLY   48 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999998874

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D Back     alignment and domain information
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial Back     alignment and domain information
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional Back     alignment and domain information
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins Back     alignment and domain information
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional Back     alignment and domain information
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Back     alignment and domain information
>PRK09391 fixK transcriptional regulator FixK; Provisional Back     alignment and domain information
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere Back     alignment and domain information
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication Back     alignment and domain information
>PRK09392 ftrB transcriptional activator FtrB; Provisional Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>smart00351 PAX Paired Box domain Back     alignment and domain information
>cd00131 PAX Paired Box domain Back     alignment and domain information
>PRK06030 hypothetical protein; Provisional Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster [] Back     alignment and domain information
>PRK13918 CRP/FNR family transcriptional regulator; Provisional Back     alignment and domain information
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities Back     alignment and domain information
>PF13518 HTH_28: Helix-turn-helix domain Back     alignment and domain information
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family Back     alignment and domain information
>PF13730 HTH_36: Helix-turn-helix domain Back     alignment and domain information
>KOG4585 consensus Predicted transposase [Replication, recombination and repair] Back     alignment and domain information
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 Back     alignment and domain information
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B Back     alignment and domain information
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs) Back     alignment and domain information
>TIGR01321 TrpR trp operon repressor, proteobacterial Back     alignment and domain information
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A Back     alignment and domain information
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif 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
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators Back     alignment and domain information
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A Back     alignment and domain information
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed Back     alignment and domain information
>PF13551 HTH_29: Winged helix-turn helix Back     alignment and domain information
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression Back     alignment and domain information
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets Back     alignment and domain information
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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
>PRK14088 dnaA chromosomal replication initiation protein; Provisional Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed Back     alignment and domain information
>PRK14086 dnaA chromosomal replication initiation protein; Provisional Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096) Back     alignment and domain information
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PRK15320 transcriptional activator SprB; Provisional Back     alignment and domain information
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional Back     alignment and domain information
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein Back     alignment and domain information
>TIGR00721 tfx DNA-binding protein, Tfx family Back     alignment and domain information
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family Back     alignment and domain information
>PRK10840 transcriptional regulator RcsB; Provisional Back     alignment and domain information
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription] Back     alignment and domain information
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B Back     alignment and domain information
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription] Back     alignment and domain information
>PRK01381 Trp operon repressor; Provisional Back     alignment and domain information
>PRK09483 response regulator; Provisional Back     alignment and domain information
>PRK14087 dnaA chromosomal replication initiation protein; Provisional Back     alignment and domain information
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PHA00738 putative HTH transcription regulator Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH Back     alignment and domain information
>PRK06930 positive control sigma-like factor; Validated Back     alignment and domain information
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation Back     alignment and domain information
>PRK09492 treR trehalose repressor; Provisional Back     alignment and domain information
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12683 transcriptional regulator CysB-like protein; Reviewed Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>PRK12422 chromosomal replication initiation protein; Provisional Back     alignment and domain information
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain Back     alignment and domain information
>PRK10651 transcriptional regulator NarL; Provisional Back     alignment and domain information
>PRK12679 cbl transcriptional regulator Cbl; Reviewed Back     alignment and domain information
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>PF13551 HTH_29: Winged helix-turn helix Back     alignment and domain information
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor Back     alignment and domain information
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia Back     alignment and domain information
>PRK15201 fimbriae regulatory protein FimW; Provisional Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor Back     alignment and domain information
>smart00153 VHP Villin headpiece domain Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor Back     alignment and domain information
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators Back     alignment and domain information
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein Back     alignment and domain information
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional Back     alignment and domain information
>PRK10403 transcriptional regulator NarP; Provisional Back     alignment and domain information
>PHA00542 putative Cro-like protein Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>PHA00675 hypothetical protein Back     alignment and domain information
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor Back     alignment and domain information
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain Back     alignment and domain information
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair] Back     alignment and domain information
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication Back     alignment and domain information
>PRK12682 transcriptional regulator CysB-like protein; Reviewed Back     alignment and domain information
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated Back     alignment and domain information
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional Back     alignment and domain information
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>TIGR02850 spore_sigG RNA polymerase sigma-G factor Back     alignment and domain information
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>TIGR03879 near_KaiC_dom probable regulatory domain Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF13309 HTH_22: HTH domain Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query91
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 96.37
2fmy_A220 COOA, carbon monoxide oxidation system transcripti 96.0
3dv8_A220 Transcriptional regulator, CRP/FNR family; cyclic 95.95
3ryp_A210 Catabolite gene activator; CAMP receptor protein ( 95.81
2oz6_A207 Virulence factor regulator; winged helix, helix-tu 95.66
2jpc_A61 SSRB; DNA binding protein, structural genomics, PS 95.64
1zyb_A232 Transcription regulator, CRP family; NP_813211.1, 95.63
3fx3_A237 Cyclic nucleotide-binding protein; helix_TURN_heli 95.63
3la7_A243 Global nitrogen regulator; activator, DNA-binding, 95.57
1ft9_A222 Carbon monoxide oxidation system transcription reg 95.57
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 95.5
1j1v_A94 Chromosomal replication initiator protein DNAA, 5' 95.47
1jhg_A101 Trp operon repressor; complex (regulatory protein- 95.46
3e6c_C250 CPRK, cyclic nucleotide-binding protein; CPRK, hal 95.37
3iwz_A230 CAP-like, catabolite activation-like protein; XCC, 95.31
3dkw_A227 DNR protein; CRP-FNR, HTH, beta barrel, dimerizati 95.17
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 95.14
3d0s_A227 Transcriptional regulatory protein; CAMP receptor 95.13
4ev0_A216 Transcription regulator, CRP family; CAMP binding, 95.08
3e97_A231 Transcriptional regulator, CRP/FNR family; YP_6044 95.02
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 94.93
2bgc_A238 PRFA; bacterial infection, human pathogen, transcr 94.83
3kcc_A260 Catabolite gene activator; helix-turn-helix, CAMP, 94.77
3c57_A95 Two component transcriptional regulatory protein; 94.75
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 94.73
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 94.73
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 94.71
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 94.71
3pvv_A101 Chromosomal replication initiator protein DNAA; he 94.43
1u78_A141 TC3 transposase, transposable element TC3 transpos 94.32
2gau_A232 Transcriptional regulator, CRP/FNR family; structu 94.24
1u78_A141 TC3 transposase, transposable element TC3 transpos 94.14
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 94.09
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 94.06
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type dom 94.03
1o5l_A213 Transcriptional regulator, CRP family; TM1171, str 93.69
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 93.41
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 93.32
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 93.02
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP 93.0
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 92.79
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 92.68
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 92.66
3b02_A195 Transcriptional regulator, CRP family; structural 92.54
2zcw_A202 TTHA1359, transcriptional regulator, FNR/CRP famil 92.38
2k27_A159 Paired box protein PAX-8; paired domain, solution 92.34
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 92.33
2jrt_A95 Uncharacterized protein; solution, structure, NESG 92.19
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-h 92.03
2lkp_A119 Transcriptional regulator, ARSR family; symmetric 91.97
3dn7_A194 Cyclic nucleotide binding regulatory protein; stru 91.84
1iuf_A144 Centromere ABP1 protein; riken structural genomics 91.15
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 90.97
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 90.95
2w7n_A101 TRFB transcriptional repressor protein; INCP, plas 90.82
2oa4_A101 SIR5; structure, structural genomics, PSI-2, prote 90.36
3cuo_A99 Uncharacterized HTH-type transcriptional regulato; 90.04
3t72_q99 RNA polymerase sigma factor RPOD, DNA-directed RN 89.61
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 89.55
1r1u_A106 CZRA, repressor protein; zinc, DNA binding, transc 89.53
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 89.47
2p5k_A64 Arginine repressor; DNA-binding domain, winged hel 89.41
1y0u_A96 Arsenical resistance operon repressor, putative; s 89.33
3frw_A107 Putative Trp repressor protein; structural genomic 89.03
2l0k_A93 Stage III sporulation protein D; SPOIIID, solution 88.83
3qp6_A265 CVIR transcriptional regulator; quorum sensing, ag 88.66
2d1h_A109 ST1889, 109AA long hypothetical transcriptional re 88.57
1l8q_A324 Chromosomal replication initiator protein DNAA; AA 88.41
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 87.65
2q0o_A236 Probable transcriptional activator protein TRAR; h 87.32
3jth_A98 Transcription activator HLYU; transcription factor 87.28
3f6o_A118 Probable transcriptional regulator, ARSR family pr 87.14
3szt_A237 QCSR, quorum-sensing control repressor; quorum sen 86.88
1ku9_A152 Hypothetical protein MJ223; putative transcription 86.66
3pqk_A102 Biofilm growth-associated repressor; helix-turn-he 86.64
2oqg_A114 Possible transcriptional regulator, ARSR family P; 86.55
3kor_A119 Possible Trp repressor; putative DNA-binding Trp r 86.46
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 86.31
2kko_A108 Possible transcriptional regulatory protein (possi 86.29
2pij_A67 Prophage PFL 6 CRO; transcription factor, helix-tu 86.07
2zkz_A99 Transcriptional repressor PAGR; protein-DNA, HTH m 86.05
1wy3_A35 Villin; structural protein; HET: NLE; 0.95A {Synth 85.72
1zx4_A 192 P1 PARB, plasmid partition PAR B protein, PARB; tr 85.6
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 85.49
2jt1_A77 PEFI protein; solution structure, winged helix-tur 85.47
1u2w_A122 CADC repressor, cadmium efflux system accessory pr 85.11
1q1h_A110 TFE, transcription factor E, TFE; TFIIE, transcrip 84.72
1und_A37 Advillin, P92; actin binding, F-actin binding, cyt 84.69
1r1t_A122 Transcriptional repressor SMTB; zinc, transcriptio 84.65
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 84.61
1a04_A215 Nitrate/nitrite response regulator protein NARL; s 84.49
1ub9_A100 Hypothetical protein PH1061; helix-turn-helix moti 84.4
3r0a_A123 Putative transcriptional regulator; structural gen 84.4
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial 83.55
1l3l_A234 Transcriptional activator protein TRAR; helix-turn 83.51
2jsc_A118 Transcriptional regulator RV1994C/MT2050; cadmium, 83.06
2x4h_A139 Hypothetical protein SSO2273; transcription; 2.30A 82.95
3ech_A142 MEXR, multidrug resistance operon repressor; winge 82.92
2k27_A159 Paired box protein PAX-8; paired domain, solution 82.72
2gxg_A146 146AA long hypothetical transcriptional regulator; 82.55
3f6v_A151 Possible transcriptional regulator, ARSR family pr 82.06
3nrv_A148 Putative transcriptional regulator (MARR/EMRR FAM; 81.49
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 81.38
1uxc_A65 FRUR (1-57), fructose repressor; DNA-binding prote 81.26
3kjx_A 344 Transcriptional regulator, LACI family; LACL famil 81.24
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 81.21
3c3w_A225 Two component transcriptional regulatory protein; 80.95
2bv6_A142 MGRA, HTH-type transcriptional regulator MGRA; mul 80.56
2frh_A127 SARA, staphylococcal accessory regulator A; winged 80.46
3bja_A139 Transcriptional regulator, MARR family, putative; 80.37
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2 Back     alignment and structure
Probab=96.37  E-value=0.0065  Score=31.52  Aligned_cols=40  Identities=20%  Similarity=0.189  Sum_probs=31.3

Q ss_pred             CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324           44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL   84 (91)
Q Consensus        44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~   84 (91)
                      .++.+++..+... ...+.+.+.|+..++.|..||+++++.
T Consensus         5 ~l~~~~~~~i~~~-~~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            4566666555544 367899999999999999999998763
>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A* Back     alignment and structure
>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656} Back     alignment and structure
>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ... Back     alignment and structure
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2 Back     alignment and structure
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} Back     alignment and structure
>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2 Back     alignment and structure
>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A* Back     alignment and structure
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A* Back     alignment and structure
>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1 Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Back     alignment and structure
>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2 Back     alignment and structure
>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A* Back     alignment and structure
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A Back     alignment and structure
>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV} Back     alignment and structure
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa} Back     alignment and structure
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} Back     alignment and structure
>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A* Back     alignment and structure
>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus} Back     alignment and structure
>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300} Back     alignment and structure
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis} Back     alignment and structure
>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A Back     alignment and structure
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli} Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_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
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Back     alignment and structure
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Back     alignment and structure
>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix motif, interacting with DNAA-BOX, DNAA-box; HET: DNA; 2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A* 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
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2 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
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Back     alignment and structure
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Back     alignment and structure
>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2 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
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Back     alignment and structure
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis} Back     alignment and structure
>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3 Back     alignment and structure
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Back     alignment and structure
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A Back     alignment and structure
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Back     alignment and structure
>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A Back     alignment and structure
>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus} Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides} Back     alignment and structure
>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3 Back     alignment and structure
>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis} Back     alignment and structure
>3dn7_A Cyclic nucleotide binding regulatory protein; structural genomics, APC88869, cyclic nucleotide binding REG protein, PSI-2; 1.80A {Cytophaga hutchinsonii} Back     alignment and structure
>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7 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
>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
>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli} Back     alignment and structure
>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3 Back     alignment and structure
>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12} Back     alignment and structure
>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Back     alignment and structure
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Back     alignment and structure
>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C* Back     alignment and structure
>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5 Back     alignment and structure
>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A Back     alignment and structure
>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis} Back     alignment and structure
>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A* Back     alignment and structure
>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50 Back     alignment and structure
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A* Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Back     alignment and structure
>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP} Back     alignment and structure
>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus} Back     alignment and structure
>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP} Back     alignment and structure
>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa} Back     alignment and structure
>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36 Back     alignment and structure
>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A Back     alignment and structure
>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP} 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
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Back     alignment and structure
>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A Back     alignment and structure
>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens} Back     alignment and structure
>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis} Back     alignment and structure
>1wy3_A Villin; structural protein; HET: NLE; 0.95A {Synthetic} PDB: 1wy4_A 1yri_A* 1yrf_A* 2f4k_A* 1vii_A 3trv_A* 3trw_A 3tjw_B* 3trv_B* 3try_A* 2ppz_A 2jm0_A* 3tjw_A* 3iur_B* 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
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2} Back     alignment and structure
>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A Back     alignment and structure
>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41 Back     alignment and structure
>1und_A Advillin, P92; actin binding, F-actin binding, cytoskeleton, headpiece subdomain; NMR {Homo sapiens} SCOP: a.14.1.1 Back     alignment and structure
>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A Back     alignment and structure
>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28 Back     alignment and structure
>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei} Back     alignment and structure
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Back     alignment and structure
>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A* Back     alignment and structure
>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus} Back     alignment and structure
>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A Back     alignment and structure
>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP} Back     alignment and structure
>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP} Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} 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
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A Back     alignment and structure
>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis} Back     alignment and structure
>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28 Back     alignment and structure
>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D Back     alignment and structure
>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus} Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query91
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 97.44
d1i5za169 Catabolite gene activator protein (CAP), C-termina 95.8
d1hlva166 DNA-binding domain of centromere binding protein B 95.63
d1ft9a180 CO-sensing protein CooA, C-terminal domain {Rhodos 95.46
d1zyba173 Probable transcription regulator BT4300, C-termina 95.36
d2gaua181 Transcriptional regulator PG0396, C-terminal domai 95.21
d1l3la165 Quorum-sensing transcription factor TraR, C-termin 93.19
d2zcwa182 Transcriptional regulator TTHA1359, C-terminal dom 93.11
d1a04a167 Nitrate/nitrite response regulator (NarL) {Escheri 92.89
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 92.67
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 92.63
d1yioa170 Response regulatory protein StyR, C-terminal domai 92.61
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 92.57
d1vz0a193 Putative partitioning protein ParB/Spo0J {Thermus 91.94
d3e5ua180 Chlorophenol reduction protein CprK {Desulfitobact 91.81
d2bgca1100 Listeriolysin regulatory protein PrfA, C-terminal 91.7
d1r1ua_94 Metal-sensing transcriptional repressor CzrA {Stap 91.56
d1r1ta_98 SmtB repressor {Cyanobacteria (Synechococcus), pcc 91.2
d1pdnc_123 Paired protein (prd) {Fruit fly (Drosophila melano 91.18
d1j1va_94 Chromosomal replication initiation factor DnaA C-t 90.73
d1l8qa1110 Chromosomal replication initiation factor DnaA C-t 90.65
d2hsga157 Glucose-resistance amylase regulator CcpA, N-termi 90.39
d1qpza157 Purine repressor (PurR), N-terminal domain {Escher 89.27
d1p4wa_87 Transcriptional regulator RcsB {Erwinia amylovora 88.53
d1s7oa_106 Hypothetical protein SPy1201 {Streptococcus pyogen 88.01
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 87.69
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 87.49
d1biaa163 Biotin repressor, N-terminal domain {Escherichia c 87.11
d2d1ha1109 Hypothetical transcriptional regulator ST1889 {Sul 85.89
d1efaa159 Lac repressor (LacR), N-terminal domain {Escherich 85.52
d1j5ya165 Putative transcriptional regulator TM1602, N-termi 84.4
d1yu8x135 Villin {Chicken (Gallus gallus) [TaxId: 9031]} 83.86
d1unda_36 Advillin {Human (Homo sapiens) [TaxId: 9606]} 83.68
d1vola195 Transcription factor IIB (TFIIB), core domain {Hum 83.11
d1uxda_59 Fructose repressor (FruR), N-terminal domain {Esch 82.52
d1d5ya154 Rob transcription factor, N-terminal domain {Esche 82.32
d1ku9a_151 DNA-binding protein Mj223 {Archaeon Methanococcus 82.27
d1jhga_101 Trp repressor, TrpR {Escherichia coli [TaxId: 562] 81.32
d1jhfa171 LexA repressor, N-terminal DNA-binding domain {Esc 81.23
d1ixca189 LysR-type regulatory protein CbnR {Ralstonia eutro 81.2
d1r71a_114 Transcriptional repressor protein KorB DNA-binding 81.2
d1xsva_106 Hypothetical protein SAV1236 {Staphylococcus aureu 81.12
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=97.44  E-value=4.9e-05  Score=41.44  Aligned_cols=36  Identities=17%  Similarity=0.174  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHH
Q 036324           47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYF   82 (91)
Q Consensus        47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f   82 (91)
                      .+||++-..-.++.|.+..+|+..|++|+.||+|||
T Consensus         7 t~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           7 NKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            357888888888999999999999999999999997
>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]} 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
>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]} Back     information, alignment and structure
>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]} Back     information, alignment and structure
>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]} Back     information, alignment and structure
>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]} Back     information, alignment and structure
>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} 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
>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]} Back     information, alignment and structure
>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]} Back     information, alignment and structure
>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]} Back     information, alignment and structure
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1j1va_ a.4.12.2 (A:) Chromosomal replication initiation factor DnaA C-terminal domain IV {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1l8qa1 a.4.12.2 (A:290-399) Chromosomal replication initiation factor DnaA C-terminal domain IV {Aquifex aeolicus [TaxId: 63363]} 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
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]} Back     information, alignment and structure
>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]} Back     information, alignment and structure
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]} Back     information, alignment and structure
>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]} 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
>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1yu8x1 a.14.1.1 (X:42-76) Villin {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1unda_ a.14.1.1 (A:) Advillin {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} 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
>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]} 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
>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]} Back     information, alignment and structure