Citrus Sinensis ID: 036926

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-------100-------110-------120-------130-------140-------150-------160-------17
ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMVSTSSCSSRHHHQVLLDADIAYDEYQITGNEDLEEMGSLFSCSSSNSIMMI
cHHHHHccccHHHHHHHccccHHHHHHHHHHccccccccHHHccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHccHHHHHHHccccccHHHHHHHHHcccccccccc
ccHHHHccccHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHcHcccHccHcccccccHHHHHHHHHHcccccEEEc
etisqyfyMPITKAAKELNVGLTLLKKRCRElnirrwphrKLMSLQTLIKNVQElqtegegsEERLREALGILERERKLieerpdlemeDTTKRLRQACFKANYKKRKfmgtmmgpmvstsscssrhhhqVLLDADIAYDEYQITGNEDLeemgslfscsssnsimmi
etisqyfympitkaaKELNVGLTLLKKRCRelnirrwphrklmsLQTLIKNVQelqtegegseerlrEALGIlererklieerpdlemedttkrLRQACFKANYKKRKFMGTMMGPMVSTSSCSSRHHHQVLLDADIAYDEYQITGNEDLEEMgslfscsssnsimmi
ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGilererklieerPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMVSTSSCSSRHHHQVLLDADIAYDEYQITGNEDLEEMGSLFSCSSSNSIMMI
****QYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNV********************************************QACFKANYKKRKFMGT**************HHHQVLLDADIAYDEYQITGN*********************
ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPH*************************************************EDTTKRLRQACFK******************************************************LFSCSSSNSIMMI
ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQE*********ERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPM**********HHQVLLDADIAYDEYQITGNEDLEEMGSLFSCS********
ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQTEGEGSEERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKANYKKRKFMGTM*******************LDADIAYDEYQITGNEDLEEMGSLFSCSSSNSIMMI
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMVSTSSCSSRHHHQVLLDADIAYDEYQITGNEDLEEMGSLFSCSSSNSIMMI
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

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query168 2.2.26 [Sep-21-2011]
Q9M9U9269 Protein RKD1 OS=Arabidops yes no 0.696 0.434 0.680 5e-40
Q9CA66298 Protein RKD2 OS=Arabidops no no 0.619 0.348 0.714 2e-38
Q9FGD1277 Protein RKD3 OS=Arabidops no no 0.666 0.404 0.640 8e-37
Q9LVU8256 Protein RKD4 OS=Arabidops no no 0.595 0.390 0.614 2e-30
O81791370 Protein RKD5 OS=Arabidops no no 0.601 0.272 0.424 2e-15
Q9M1B0 894 Protein NLP9 OS=Arabidops no no 0.392 0.073 0.348 7e-05
Q7X9B9 963 Protein NLP2 OS=Arabidops no no 0.333 0.058 0.412 9e-05
Q9SFW8808 Protein NLP5 OS=Arabidops no no 0.363 0.075 0.344 0.0002
Q8H111 909 Protein NLP1 OS=Arabidops no no 0.398 0.073 0.328 0.0003
Q9SVF1767 Protein NLP3 OS=Arabidops no no 0.410 0.089 0.333 0.0004
>sp|Q9M9U9|RKD1_ARATH Protein RKD1 OS=Arabidopsis thaliana GN=RKD1 PE=3 SV=1 Back     alignment and function desciption
 Score =  163 bits (412), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 81/119 (68%), Positives = 99/119 (83%), Gaps = 2/119 (1%)

Query: 1   ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQT-EG 59
           ETIS YFYMPIT+AA+ELN+GLTLLKKRCREL I+RWPHRKLMSLQ LI NV+EL+  EG
Sbjct: 131 ETISLYFYMPITQAARELNIGLTLLKKRCRELGIKRWPHRKLMSLQKLISNVKELEKMEG 190

Query: 60  EGSEERLREALGILERERKLIEERPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMV 118
           E +E++LR AL  LE+E+K IE+ PDL+ ED TKRLRQACFKAN+K+++  G M  P+ 
Sbjct: 191 EENEDKLRNALEKLEKEKKTIEKLPDLKFEDKTKRLRQACFKANHKRKRRSG-MSTPIT 248
Putative transcription factor.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9CA66|RKD2_ARATH Protein RKD2 OS=Arabidopsis thaliana GN=RKD2 PE=2 SV=1 Back     alignment and function description
>sp|Q9FGD1|RKD3_ARATH Protein RKD3 OS=Arabidopsis thaliana GN=RKD3 PE=3 SV=1 Back     alignment and function description
>sp|Q9LVU8|RKD4_ARATH Protein RKD4 OS=Arabidopsis thaliana GN=RKD4 PE=3 SV=1 Back     alignment and function description
>sp|O81791|RKD5_ARATH Protein RKD5 OS=Arabidopsis thaliana GN=RKD5 PE=3 SV=1 Back     alignment and function description
>sp|Q9M1B0|NLP9_ARATH Protein NLP9 OS=Arabidopsis thaliana GN=NLP9 PE=2 SV=1 Back     alignment and function description
>sp|Q7X9B9|NLP2_ARATH Protein NLP2 OS=Arabidopsis thaliana GN=NLP2 PE=2 SV=3 Back     alignment and function description
>sp|Q9SFW8|NLP5_ARATH Protein NLP5 OS=Arabidopsis thaliana GN=NLP5 PE=2 SV=1 Back     alignment and function description
>sp|Q8H111|NLP1_ARATH Protein NLP1 OS=Arabidopsis thaliana GN=NLP1 PE=2 SV=1 Back     alignment and function description
>sp|Q9SVF1|NLP3_ARATH Protein NLP3 OS=Arabidopsis thaliana GN=NLP3 PE=2 SV=1 Back     alignment and function description

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 ?
Query168
225457411 305 PREDICTED: protein RKD2-like [Vitis vini 0.928 0.511 0.644 5e-45
297733972 497 unnamed protein product [Vitis vinifera] 0.666 0.225 0.807 3e-44
356513529 305 PREDICTED: uncharacterized protein LOC10 0.732 0.403 0.741 3e-44
255547389 312 transcription factor, putative [Ricinus 0.928 0.5 0.622 5e-44
356519060268 PREDICTED: protein RKD2-like [Glycine ma 0.744 0.466 0.674 2e-41
356507131 280 PREDICTED: uncharacterized protein LOC10 0.660 0.396 0.714 3e-40
449477581242 PREDICTED: protein RKD1-like [Cucumis sa 0.660 0.458 0.709 6e-40
297842195 298 RWP-RK domain-containing protein [Arabid 0.619 0.348 0.752 1e-38
297850268259 RWP-RK domain-containing protein [Arabid 0.696 0.451 0.680 1e-38
15221874 269 RWP-RK domain-containing protein [Arabid 0.696 0.434 0.680 3e-38
>gi|225457411|ref|XP_002282066.1| PREDICTED: protein RKD2-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  185 bits (470), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 109/169 (64%), Positives = 130/169 (76%), Gaps = 13/169 (7%)

Query: 2   TISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQEL-QTEGE 60
           TISQYFYMPIT+AA+EL VGLTLLKKRCREL IRRWPHRKLMSLQTLIKNVQEL + EG+
Sbjct: 148 TISQYFYMPITQAARELKVGLTLLKKRCRELGIRRWPHRKLMSLQTLIKNVQELGKDEGD 207

Query: 61  GSEE-RLREALGILERERKLIEERPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMVS 119
           GS++ +LREA+ ILE+ERKL+EE PDL++ED TKRLRQA FKANYKKRK MGTM      
Sbjct: 208 GSDQGKLREAIQILEQERKLMEEMPDLQLEDKTKRLRQAYFKANYKKRKLMGTM-----D 262

Query: 120 TSSCSSRHHHQVLLDADIAYDEYQITGNEDLEEMGSLFSCSSSNSIMMI 168
           +S  SS  + Q +   ++A + Y     ED  EM SL S S S++ MM+
Sbjct: 263 SSQSSSNSNPQTV---EVAMN-YTTMDEED--EMKSLLSDSFSSTNMML 305

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|297733972|emb|CBI15219.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|356513529|ref|XP_003525466.1| PREDICTED: uncharacterized protein LOC100788666 [Glycine max] Back     alignment and taxonomy information
>gi|255547389|ref|XP_002514752.1| transcription factor, putative [Ricinus communis] gi|223546356|gb|EEF47858.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|356519060|ref|XP_003528192.1| PREDICTED: protein RKD2-like [Glycine max] Back     alignment and taxonomy information
>gi|356507131|ref|XP_003522324.1| PREDICTED: uncharacterized protein LOC100782238, partial [Glycine max] Back     alignment and taxonomy information
>gi|449477581|ref|XP_004155063.1| PREDICTED: protein RKD1-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297842195|ref|XP_002888979.1| RWP-RK domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297334820|gb|EFH65238.1| RWP-RK domain-containing protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|297850268|ref|XP_002893015.1| RWP-RK domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297338857|gb|EFH69274.1| RWP-RK domain-containing protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15221874|ref|NP_173314.1| RWP-RK domain-containing protein [Arabidopsis thaliana] gi|75191562|sp|Q9M9U9.1|RKD1_ARATH RecName: Full=Protein RKD1; Short=AtRKD1; AltName: Full=RWP-RK domain-containing protein 1 gi|6730706|gb|AAF27101.1|AC011809_10 Hypothetical protein [Arabidopsis thaliana] gi|332191643|gb|AEE29764.1| RWP-RK domain-containing protein [Arabidopsis thaliana] 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 ?
Query168
TAIR|locus:2035000269 RKD1 "RWP-RK domain containing 0.738 0.460 0.626 7.2e-36
TAIR|locus:2019175298 RKD2 "RWP-RK domain containing 0.916 0.516 0.530 1.7e-34
TAIR|locus:2158113277 RKD3 "RWP-RK domain-containing 0.666 0.404 0.578 1.3e-29
TAIR|locus:2168412256 RKD4 "RWP-RK domain-containing 0.595 0.390 0.559 5.9e-25
TAIR|locus:2127908370 RKD5 "RWP-RK domain-containing 0.726 0.329 0.341 1.1e-12
DICTYBASE|DDB_G0274295 548 DDB_G0274295 "RWP-RK domain-co 0.416 0.127 0.414 9.2e-12
TAIR|locus:2035000 RKD1 "RWP-RK domain containing 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 79/126 (62%), Positives = 96/126 (76%)

Query:     1 ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSLQTLIKNVQELQT-EG 59
             ETIS YFYMPIT+AA+ELN+GLTLLKKRCREL I+RWPHRKLMSLQ LI NV+EL+  EG
Sbjct:   131 ETISLYFYMPITQAARELNIGLTLLKKRCRELGIKRWPHRKLMSLQKLISNVKELEKMEG 190

Query:    60 EGSEERLREALGXXXXXXXXXXXXPDLEMEDTTKRLRQACFKANYKKRKFMGTMMGPMVS 119
             E +E++LR AL             PDL+ ED TKRLRQACFKAN+K+++  G M  P+ S
Sbjct:   191 EENEDKLRNALEKLEKEKKTIEKLPDLKFEDKTKRLRQACFKANHKRKRRSG-MSTPITS 249

Query:   120 TSSCSS 125
             +SS +S
Sbjct:   250 SSSSAS 255
GO:0005634 "nucleus" evidence=ISM
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS
GO:0051302 "regulation of cell division" evidence=IMP
TAIR|locus:2019175 RKD2 "RWP-RK domain containing 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2158113 RKD3 "RWP-RK domain-containing 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2168412 RKD4 "RWP-RK domain-containing 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2127908 RKD5 "RWP-RK domain-containing 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0274295 DDB_G0274295 "RWP-RK domain-containing protein" [Dictyostelium discoideum (taxid:44689)] 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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
pfam0204252 pfam02042, RWP-RK, RWP-RK domain 2e-24
>gnl|CDD|190197 pfam02042, RWP-RK, RWP-RK domain Back     alignment and domain information 
 Score = 89.2 bits (222), Expect = 2e-24
 Identities = 29/45 (64%), Positives = 37/45 (82%)

Query: 1  ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL 45
          E +S+YF++PI  AAKEL VGLT+LK+ CR+L I RWPHRK+ SL
Sbjct: 8  EDLSKYFHLPIKDAAKELGVGLTVLKRICRQLGIPRWPHRKIKSL 52

This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. Length = 52

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 168
PF0204252 RWP-RK: RWP-RK domain; InterPro: IPR003035 This do 99.93
PF0141877 HTH_6: Helix-turn-helix domain, rpiR family; Inter 96.46
TIGR0176449 excise DNA binding domain, excisionase family. An 95.94
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 95.58
PF1272851 HTH_17: Helix-turn-helix domain 95.27
cd0476249 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain 95.24
cd0476149 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of 95.18
PF0295442 HTH_8: Bacterial regulatory protein, Fis family; I 95.07
cd0476368 HTH_MlrA-like Helix-Turn-Helix DNA binding domain 95.07
cd0476467 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom 95.04
PRK11302284 DNA-binding transcriptional regulator HexR; Provis 94.95
PRK15482285 transcriptional regulator MurR; Provisional 94.8
cd0476599 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom 94.62
COG1737281 RpiR Transcriptional regulators [Transcription] 94.33
cd0110468 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain 94.23
PRK11557278 putative DNA-binding transcriptional regulator; Pr 93.93
PRK0043095 fis global DNA-binding transcriptional dual regula 93.92
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 93.79
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 93.76
PRK11337292 DNA-binding transcriptional repressor RpiR; Provis 93.73
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 93.26
smart0034284 HTH_ARAC helix_turn_helix, arabinose operon contro 93.14
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 92.9
PRK09413121 IS2 repressor TnpA; Reviewed 92.85
PRK13182175 racA polar chromosome segregation protein; Reviewe 92.8
PRK0190577 DNA-binding protein Fis; Provisional 92.65
cd01106103 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain 92.58
cd04776118 HTH_GnyR Helix-Turn-Helix DNA binding domain of th 92.43
smart0042270 HTH_MERR helix_turn_helix, mercury resistance. 92.13
PF02001106 DUF134: Protein of unknown function DUF134; InterP 92.07
PF1341169 MerR_1: MerR HTH family regulatory protein; PDB: 2 91.95
cd04789102 HTH_Cfa Helix-Turn-Helix DNA binding domain of the 91.63
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 91.59
PF0016542 HTH_AraC: Bacterial regulatory helix-turn-helix pr 91.41
cd0477496 HTH_YfmP Helix-Turn-Helix DNA binding domain of th 91.23
PF01710119 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr 90.94
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 90.82
cd0476691 HTH_HspR Helix-Turn-Helix DNA binding domain of th 90.81
PF1351852 HTH_28: Helix-turn-helix domain 90.7
cd01109113 HTH_YyaN Helix-Turn-Helix DNA binding domain of th 90.66
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 90.17
PF0138155 HTH_3: Helix-turn-helix; InterPro: IPR001387 This 90.12
PRK10219107 DNA-binding transcriptional regulator SoxS; Provis 89.88
cd01282112 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom 89.76
cd04787133 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain 89.73
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 89.41
PF1340442 HTH_AsnC-type: AsnC-type helix-turn-helix domain; 89.35
PF0745337 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he 89.13
smart0049753 IENR1 Intron encoded nuclease repeat motif. Repeat 88.81
cd0478896 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain 88.72
TIGR0253188 yecD_yerC TrpR-related protein YerC/YecD. This mod 88.57
PF03374111 ANT: Phage antirepressor protein KilAC domain; Int 88.21
cd0110588 HTH_GlnR-like Helix-Turn-Helix DNA binding domain 87.92
PF0522545 HTH_psq: helix-turn-helix, Psq domain; InterPro: I 87.75
PF0368376 UPF0175: Uncharacterised protein family (UPF0175); 87.65
TIGR0307058 couple_hipB transcriptional regulator, y4mF family 87.5
cd04785126 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do 87.2
cd04790172 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma 86.95
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 86.72
PF1356064 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_ 86.67
TIGR02047127 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional 86.35
PF0605658 Terminase_5: Putative ATPase subunit of terminase 86.33
PRK14101 638 bifunctional glucokinase/RpiR family transcription 86.22
PRK15043243 transcriptional regulator MirA; Provisional 86.11
cd0478297 HTH_BltR Helix-Turn-Helix DNA binding domain of th 86.02
cd04775102 HTH_Cfa-like Helix-Turn-Helix DNA binding domain o 85.84
cd04773108 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding 85.77
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 85.63
PRK12533216 RNA polymerase sigma factor; Provisional 85.44
PF0476054 IF2_N: Translation initiation factor IF-2, N-termi 85.4
cd00592100 HTH_MerR-like Helix-Turn-Helix DNA binding domain 85.19
PF1284464 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_ 85.07
cd0127998 HTH_HspR-like Helix-Turn-Helix DNA binding domain 85.02
cd0476896 HTH_BmrR-like Helix-Turn-Helix DNA binding domain 84.96
PF1301185 LZ_Tnp_IS481: leucine-zipper of insertion element 84.93
PRK11511127 DNA-binding transcriptional activator MarA; Provis 84.84
PRK12511182 RNA polymerase sigma factor; Provisional 84.67
cd01108127 HTH_CueR Helix-Turn-Helix DNA binding domain of Cu 84.62
PRK04217110 hypothetical protein; Provisional 84.55
TIGR0132194 TrpR trp operon repressor, proteobacterial. This m 84.37
PF1344363 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3 84.34
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR- 84.24
PF0035646 LacI: Bacterial regulatory proteins, lacI family; 84.07
TIGR02297287 HpaA 4-hydroxyphenylacetate catabolism regulatory 83.74
cd01110139 HTH_SoxR Helix-Turn-Helix DNA binding domain of th 83.21
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 83.15
smart0035470 HTH_LACI helix_turn _helix lactose operon represso 83.06
COG1522154 Lrp Transcriptional regulators [Transcription] 82.99
cd01107108 HTH_BmrR Helix-Turn-Helix DNA binding domain of th 82.98
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 82.37
PRK00118104 putative DNA-binding protein; Validated 82.3
COG147668 Predicted transcriptional regulators [Transcriptio 82.3
COG134299 Predicted DNA-binding proteins [General function p 82.08
PF0137187 Trp_repressor: Trp repressor protein; InterPro: IP 81.63
PHA0197667 helix-turn-helix protein 81.38
PRK09636293 RNA polymerase sigma factor SigJ; Provisional 81.34
PF1374480 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_ 81.22
smart0034560 HTH_GNTR helix_turn_helix gluconate operon transcr 81.12
PF0149872 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Tr 81.06
PF1283381 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_ 80.98
TIGR0260778 antidote_HigA addiction module antidote protein, H 80.97
PRK09514140 zntR zinc-responsive transcriptional regulator; Pr 80.96
PRK12516187 RNA polymerase sigma factor; Provisional 80.9
TIGR02044127 CueR Cu(I)-responsive transcriptional regulator. T 80.89
PF13551112 HTH_29: Winged helix-turn helix 80.71
PF0697076 RepA_N: Replication initiator protein A (RepA) N-t 80.7
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family. Thi 80.58
PRK08241339 RNA polymerase factor sigma-70; Validated 80.53
PF1066860 Phage_terminase: Phage terminase small subunit; In 80.5
PF0593051 Phage_AlpA: Prophage CP4-57 regulatory protein (Al 80.38
smart00351125 PAX Paired Box domain. 80.07
PRK09635290 sigI RNA polymerase sigma factor SigI; Provisional 80.03
TIGR0387973 near_KaiC_dom probable regulatory domain. This mod 80.01
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain Back     alignment and domain information 
Probab=99.93  E-value=3.8e-27  Score=160.11  Aligned_cols=45  Identities=64%  Similarity=1.051  Sum_probs=43.8

Q ss_pred             ChhhhhccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhhhcH
Q 036926            1 ETISQYFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKLMSL   45 (168)
Q Consensus         1 e~l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKlkSL   45 (168)
                      |||++|||||++|||++||||+|+|||+||++||+||||||++||
T Consensus         8 ~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl~Sl   52 (52)
T PF02042_consen    8 EDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKLKSL   52 (52)
T ss_pred             HHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhhccC
Confidence            589999999999999999999999999999999999999999986

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif [] Back     alignment and domain information
>TIGR01764 excise DNA binding domain, excisionase family 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
>PF12728 HTH_17: Helix-turn-helix domain 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
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily Back     alignment and domain information
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,] Back     alignment and domain information
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators Back     alignment and domain information
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators Back     alignment and domain information
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional Back     alignment and domain information
>PRK15482 transcriptional regulator MurR; Provisional Back     alignment and domain information
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators Back     alignment and domain information
>COG1737 RpiR Transcriptional regulators [Transcription] Back     alignment and domain information
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA Back     alignment and domain information
>PRK11557 putative DNA-binding transcriptional regulator; Provisional Back     alignment and domain information
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional 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
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed Back     alignment and domain information
>PRK13182 racA polar chromosome segregation protein; Reviewed Back     alignment and domain information
>PRK01905 DNA-binding protein Fis; Provisional Back     alignment and domain information
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA Back     alignment and domain information
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR Back     alignment and domain information
>smart00422 HTH_MERR helix_turn_helix, mercury resistance Back     alignment and domain information
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function Back     alignment and domain information
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B Back     alignment and domain information
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator Back     alignment and domain information
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 Back     alignment and domain information
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A Back     alignment and domain information
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator 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
>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
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator Back     alignment and domain information
>PF13518 HTH_28: Helix-turn-helix domain Back     alignment and domain information
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB 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
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould) Back     alignment and domain information
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional Back     alignment and domain information
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily Back     alignment and domain information
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators Back     alignment and domain information
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B Back     alignment and domain information
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [] Back     alignment and domain information
>smart00497 IENR1 Intron encoded nuclease repeat motif Back     alignment and domain information
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR Back     alignment and domain information
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD Back     alignment and domain information
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain Back     alignment and domain information
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators 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
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function Back     alignment and domain information
>TIGR03070 couple_hipB transcriptional regulator, y4mF family Back     alignment and domain information
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators Back     alignment and domain information
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators 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
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A Back     alignment and domain information
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator Back     alignment and domain information
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after [] Back     alignment and domain information
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional Back     alignment and domain information
>PRK15043 transcriptional regulator MirA; Provisional Back     alignment and domain information
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator Back     alignment and domain information
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators Back     alignment and domain information
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2 Back     alignment and domain information
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators Back     alignment and domain information
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B Back     alignment and domain information
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators Back     alignment and domain information
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators Back     alignment and domain information
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481 Back     alignment and domain information
>PRK11511 DNA-binding transcriptional activator MarA; Provisional Back     alignment and domain information
>PRK12511 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>TIGR01321 TrpR trp operon repressor, proteobacterial Back     alignment and domain information
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins 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
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA Back     alignment and domain information
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator 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
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor Back     alignment and domain information
>COG1522 Lrp Transcriptional regulators [Transcription] Back     alignment and domain information
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator 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
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>COG1476 Predicted transcriptional regulators [Transcription] Back     alignment and domain information
>COG1342 Predicted DNA-binding proteins [General function prediction only] 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
>PHA01976 helix-turn-helix protein Back     alignment and domain information
>PRK09636 RNA polymerase sigma factor SigJ; Provisional Back     alignment and domain information
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A Back     alignment and domain information
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor Back     alignment and domain information
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B Back     alignment and domain information
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family Back     alignment and domain information
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator Back     alignment and domain information
>PF13551 HTH_29: Winged helix-turn helix Back     alignment and domain information
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids [] Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>PRK08241 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes Back     alignment and domain information
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88 Back     alignment and domain information
>smart00351 PAX Paired Box domain Back     alignment and domain information
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional Back     alignment and domain information
>TIGR03879 near_KaiC_dom probable regulatory 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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query168
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-04
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
 Score = 40.6 bits (94), Expect = 1e-04
 Identities = 18/166 (10%), Positives = 50/166 (30%), Gaps = 22/166 (13%)

Query: 1   ETISQYFYMPITKAAKELNVG----LTLLKKRCRELNIR--RWPHRKLMSLQTLIKNVQE 54
             + +Y         +E+       L+++ +  R+       W H     L T+I++   
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364

Query: 55  LQTEGEGSEERLREALGILERERKL---------IEERPDLEMEDTTKRLRQACFKANYK 105
           +    E    ++ + L +      +          +      M    K  + +  +   K
Sbjct: 365 VLEPAE--YRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422

Query: 106 KRKFMGTMMGPMVSTSSCSSRH-HHQVLLDADIAYDEYQITGNEDL 150
           +          +       + +  H+ ++D       +    ++DL
Sbjct: 423 ESTI-SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD---SDDL 464

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query168
2o3f_A111 Putative HTH-type transcriptional regulator YBBH; 96.53
3e7l_A63 Transcriptional regulator (NTRC family); sigma43 a 96.33
1g2h_A61 Transcriptional regulatory protein TYRR homolog; p 96.1
3iwf_A107 Transcription regulator RPIR family; transcription 95.93
1umq_A81 Photosynthetic apparatus regulatory protein; DNA-b 95.41
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 95.27
1eto_A98 FIS, factor for inversion stimulation; transcripti 94.84
1ntc_A91 Protein (nitrogen regulation protein (NTRC)); heli 94.82
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 94.8
1j9i_A68 GPNU1 DBD;, terminase small subunit; DNA binding d 93.82
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 92.86
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 92.63
3lsg_A103 Two-component response regulator YESN; structural 92.44
2k9s_A107 Arabinose operon regulatory protein; activator, ar 92.44
2jml_A81 DNA binding domain/transcriptional regulator; anti 92.3
3oou_A108 LIN2118 protein; protein structure initiative, PSI 91.65
3mkl_A120 HTH-type transcriptional regulator GADX; PSI2, MCS 91.18
3mn2_A108 Probable ARAC family transcriptional regulator; st 90.93
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 90.27
3oio_A113 Transcriptional regulator (ARAC-type DNA-binding c 90.24
1r8d_A109 Transcription activator MTAN; protein-DNA complex, 90.16
2xi8_A66 Putative transcription regulator; HTH DNA-binding 90.03
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 89.79
2vz4_A108 Tipal, HTH-type transcriptional activator TIPA; tr 89.68
1y6u_A70 XIS, excisionase from transposon TN916; structure, 89.65
1u78_A141 TC3 transposase, transposable element TC3 transpos 89.5
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 89.2
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 88.78
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 88.66
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-h 88.59
2jpc_A61 SSRB; DNA binding protein, structural genomics, PS 88.4
1bl0_A129 Protein (multiple antibiotic resistance protein), 88.16
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 87.66
2b5a_A77 C.BCLI; helix-turn-helix motif, gene regulation; 1 87.59
3b7h_A78 Prophage LP1 protein 11; structural genomics, PSI2 87.58
3fmy_A73 HTH-type transcriptional regulator MQSA (YGIT/B302 87.53
2r1j_L68 Repressor protein C2; protein-DNA complex, helix-t 87.34
1z4h_A66 TORI, TOR inhibition protein; winged helix, revers 87.22
1uxc_A65 FRUR (1-57), fructose repressor; DNA-binding prote 87.15
1zug_A71 Phage 434 CRO protein; gene regulating protein, tr 86.89
3o9x_A133 Uncharacterized HTH-type transcriptional regulato; 86.86
3omt_A73 Uncharacterized protein; structural genomics, PSI- 86.85
3bs3_A76 Putative DNA-binding protein; XRE-family, structur 86.84
1y7y_A74 C.AHDI; helix-turn-helix, DNA-binding protein, tra 86.63
1adr_A76 P22 C2 repressor; transcription regulation; NMR {E 86.44
1r69_A69 Repressor protein CI; gene regulating protein; 2.0 86.43
3s8q_A82 R-M controller protein; protein-DNA complex, helix 86.39
3t76_A88 VANU, transcriptional regulator vanug; structural 86.35
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 86.11
2wiu_B88 HTH-type transcriptional regulator HIPB; transfera 85.56
2kpj_A94 SOS-response transcriptional repressor, LEXA; NESG 85.56
2k9q_A77 Uncharacterized protein; all helix, helix-turn-hel 85.49
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 85.32
3gpv_A148 Transcriptional regulator, MERR family; protein st 85.31
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 85.25
2ef8_A84 C.ECOT38IS, putative transcription factor; helix-t 85.14
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 85.06
3bd1_A79 CRO protein; transcription factor, helix-turn-heli 84.96
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 84.68
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 84.42
1jhg_A101 Trp operon repressor; complex (regulatory protein- 84.34
3gbg_A276 TCP pilus virulence regulatory protein; cupin, hel 84.28
2ewt_A71 BLDD, putative DNA-binding protein; the DNA-bindin 84.22
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 83.91
3qq6_A78 HTH-type transcriptional regulator SINR; helix-tur 83.83
1b0n_A111 Protein (SINR protein); transcription regulator, a 83.76
2a6c_A83 Helix-turn-helix motif; putative transcriptional r 83.1
3f6w_A83 XRE-family like protein; helix-turn-helix, DNA bin 83.09
3kz3_A80 Repressor protein CI; five helix bundle, DNA-bindi 83.0
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 83.0
3op9_A114 PLI0006 protein; structural genomics, PSI-2, prote 82.94
3c57_A95 Two component transcriptional regulatory protein; 82.58
3gp4_A142 Transcriptional regulator, MERR family; structural 82.51
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 82.41
2ppx_A99 AGR_C_3184P, uncharacterized protein ATU1735; HTH- 82.38
1q06_A135 Transcriptional regulator CUER; MERR family transc 82.12
3eus_A86 DNA-binding protein; structural genomics, PSI2,MCS 81.89
2eby_A113 Putative HTH-type transcriptional regulator YBAQ; 81.8
2cw1_A65 SN4M; lambda CRO fold, de novo protein; NMR {Synth 81.78
1lmb_392 Protein (lambda repressor); protein-DNA complex, d 81.58
2ict_A94 Antitoxin HIGA; helix-turn-helix, structural genom 81.18
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP 81.11
3qao_A249 LMO0526 protein, MERR-like transcriptional regulat 80.84
1x57_A91 Endothelial differentiation-related factor 1; HMBF 80.61
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 80.54
2pij_A67 Prophage PFL 6 CRO; transcription factor, helix-tu 80.15
1zx4_A192 P1 PARB, plasmid partition PAR B protein, PARB; tr 80.13
>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20 Back     alignment and structure
Probab=96.53  E-value=0.0014  Score=48.12  Aligned_cols=37  Identities=8%  Similarity=0.167  Sum_probs=32.5

Q ss_pred             hccCcHHHHHHHcCCChhHHHHHHHHcCCCCCCchhh
Q 036926            6 YFYMPITKAAKELNVGLTLLKKRCRELNIRRWPHRKL   42 (168)
Q Consensus         6 yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~RWP~RKl   42 (168)
                      ..++++.+.|++.|||.+++-|.||++|...|+-=|.
T Consensus        37 ~~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~efk~   73 (111)
T 2o3f_A           37 AIESTVNEISALANSSDAAVIRLCXSLGLKGFQDLXM   73 (111)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHH
T ss_pred             HHhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHH
Confidence            3579999999999999999999999999988875443
>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A Back     alignment and structure
>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12 Back     alignment and structure
>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis} Back     alignment and structure
>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
>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ... Back     alignment and structure
>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12 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
>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5 Back     alignment and structure
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} 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
>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum} Back     alignment and structure
>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli} Back     alignment and structure
>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus} Back     alignment and structure
>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua} Back     alignment and structure
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli} Back     alignment and structure
>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris} 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
>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum} Back     alignment and structure
>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A Back     alignment and structure
>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_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
>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans} Back     alignment and structure
>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis} 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
>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
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} 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
>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
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} Back     alignment and structure
>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_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
>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3 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
>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
>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
>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli} 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
>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
>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* 2kz8_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
>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis} 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
>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 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
>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A* Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Back     alignment and structure
>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* 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
>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron} 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
>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian} 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
>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
>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
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa} 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
>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP} 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
>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae} Back     alignment and structure
>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor} 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
>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis} 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 PDB: 2yal_A 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
>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} 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
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} 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
>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
>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str} 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
>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
>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A Back     alignment and structure
>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi} 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
>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1 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
>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A 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
>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes} 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
>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
>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens} 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

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 ?
Query168
d1g2ha_61 Transcriptional regulator TyrR, C-terminal domain 96.95
d1umqa_60 Photosynthetic apparatus regulatory protein PprA ( 96.04
d2o3fa183 Putative transcriptional regulator YbbH {Bacillus 96.04
d1ntca_91 DNA-binding domain of NTRC {Salmonella typhimurium 95.3
d1etxa_89 FIS protein {Escherichia coli [TaxId: 562]} 95.21
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 93.51
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 93.11
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 91.93
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 91.15
d2ppxa162 Uncharacterized protein Atu1735 {Agrobacterium tum 88.74
d1a04a167 Nitrate/nitrite response regulator (NarL) {Escheri 88.46
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 87.29
d2hsga157 Glucose-resistance amylase regulator CcpA, N-termi 86.79
d1yioa170 Response regulatory protein StyR, C-terminal domai 86.35
d1bl0a154 MarA {Escherichia coli [TaxId: 562]} 86.25
d1i3ja_96 DNA-binding domain of intron endonuclease I-TevI { 86.13
d2cfxa163 Transcriptional regulator LrpC {Bacillus subtilis 85.87
d2auwa167 Hypothetical protein NE0471 C-terminal domain {Nit 85.61
d1b0na268 SinR repressor, DNA-binding domain {Bacillus subti 84.93
d2cyya160 Putative transcriptional regulator PH1519 {Archaeo 84.75
d1r69a_63 434 C1 repressor, DNA-binding domain {Bacteriophag 84.63
d1d5ya154 Rob transcription factor, N-terminal domain {Esche 84.41
d2cg4a163 Regulatory protein AsnC {Escherichia coli [TaxId: 84.38
d1xsva_106 Hypothetical protein SAV1236 {Staphylococcus aureu 84.36
d2icta187 Antitoxin HigA {Escherichia coli [TaxId: 562]} 83.71
d1s7oa_106 Hypothetical protein SPy1201 {Streptococcus pyogen 83.16
d2a6ca169 HTH-motif protein NE1354 {Nitrosomonas europaea [T 82.63
d2b5aa177 Regulatory protein C.BclI {Bacillus caldolyticus [ 82.62
d2hs5a169 Putative transcriptional regulator RHA1_ro03477 {R 81.22
d1utxa_66 Putative transcription regulator CylR2 {Enterococc 80.72
d1l3la165 Quorum-sensing transcription factor TraR, C-termin 80.26
>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.95  E-value=0.00034  Score=45.59  Aligned_cols=32  Identities=22%  Similarity=0.368  Sum_probs=27.6

Q ss_pred             hhhhccCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 036926            3 ISQYFYMPITKAAKELNVGLTLLKKRCRELNIRR   36 (168)
Q Consensus         3 l~~yF~lPi~eAAr~LgVs~T~LKr~CR~lGI~R   36 (168)
                      |.++ + -..+||+.|||+.++|-+..+++||.|
T Consensus        30 L~~~-g-n~~~aA~~Lgisr~tL~rKlkk~gi~k   61 (61)
T d1g2ha_          30 YAEY-P-STRKLAQRLGVSHTAIANKLKQYGIGK   61 (61)
T ss_dssp             HHHS-C-SHHHHHHHTTSCTHHHHHHHHTTTCCC
T ss_pred             HHHC-C-CHHHHHHHHCCCHHHHHHHHHHhCCCC
Confidence            4444 4 578999999999999999999999975
>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]} Back     information, alignment and structure
>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure
>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} 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
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} 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
>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {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
>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
>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1i3ja_ d.285.1.1 (A:) DNA-binding domain of intron endonuclease I-TevI {Bacteriophage T4 [TaxId: 10665]} Back     information, alignment and structure
>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure
>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]} Back     information, alignment and structure
>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {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
>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]} Back     information, alignment and structure
>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure
>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Back     information, alignment and structure
>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]} Back     information, alignment and structure
>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} 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