Citrus Sinensis ID: 046385

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-------170-------180-------190-------200-------210-------22
MAMADEEVDIKIGVRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTDQMGKSKGHHQDFGGSRCPINDIVGTGLGPSRQ
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHccHHHHHHHccccHHHHHHHHHHHHHHccccccccEEHHHHHHHHHHHHHHcccHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHccccHHHHHHHcccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHccccccccccccccccccHccccccccHHHccEEEEcccEEEEEEEEEccccccccccccccc
mamadeevDIKIGVRRILRKQLIMLVKKLLKgstkrqrvstssltgSLYIQELlngspifcydlmrmdkNGFISLCQLFKekgwlsdskhLTVEEKMAMFLFTISHNLRNRFIKIrfqhsghtVHRYFHEVLSAMMKFSkemitppsftdnsrgirNTRLRQifkrspvvplnlqkmsrmpqfltdqmgkskghhqdfggsrcpindivgtglgpsrq
mamadeevdikigvrrilRKQLIMLVKkllkgstkrqrvstssltgslyiQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMItppsftdnsrgirntrlrqifkrspvvplnlqkMSRMPQFLTDQMGKSKGHhqdfggsrcpindivgtglgpsrq
MAMADEEVDIKIGVRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTDQMGKSKGHHQDFGGSRCPINDIVGTGLGPSRQ
*******VDIKIGVRRILRKQLIMLVKKLLKGST****V*TSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMI***************RLRQIFK***V*************************************************
*************VRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTDQMGKSKGHHQDFGGSRCPINDIV*********
MAMADEEVDIKIGVRRILRKQLIMLVKKL**************LTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTD***********FGGSRCPINDIVGTGLGPSRQ
****DEEVDIKIGVRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTDQMGKSKGHHQDFGGSRCPINDIV*********
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MAMADEEVDIKIGVRRILRKQLIMLVKKLLKGSTKRQRVSTSSLTGSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFKRSPVVPLNLQKMSRMPQFLTDQMGKSKGHHQDFGGSRCPINDIVGTGLGPSRQ
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 ?
Query218
147771935 596 hypothetical protein VITISV_035983 [Viti 0.550 0.201 0.766 1e-48
147861273 599 hypothetical protein VITISV_041568 [Viti 0.559 0.203 0.754 2e-48
147852015 592 hypothetical protein VITISV_039752 [Viti 0.596 0.219 0.707 8e-48
147792468 352 hypothetical protein VITISV_036360 [Viti 0.587 0.363 0.710 2e-46
147842396 749 hypothetical protein VITISV_020305 [Viti 0.490 0.142 0.623 6e-33
225463187 391 PREDICTED: putative nuclease HARBI1-like 0.614 0.342 0.402 6e-22
356530983 481 PREDICTED: uncharacterized protein LOC10 0.536 0.243 0.401 5e-20
255553963 354 hypothetical protein RCOM_1176900 [Ricin 0.587 0.361 0.407 6e-20
147772236 354 hypothetical protein VITISV_020377 [Viti 0.348 0.214 0.602 1e-19
115474393 629 Os08g0106900 [Oryza sativa Japonica Grou 0.481 0.166 0.438 1e-19
>gi|147771935|emb|CAN75696.1| hypothetical protein VITISV_035983 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  198 bits (503), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 92/120 (76%), Positives = 102/120 (85%)

Query: 46  GSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLTVEEKMAMFLFTIS 105
           GSL+IQELLNGS   CY+LMRM+K+GFISLC +F+EKGWL DSKHL VEEKM MFL TIS
Sbjct: 252 GSLFIQELLNGSSSTCYELMRMEKHGFISLCHMFREKGWLVDSKHLNVEEKMTMFLMTIS 311

Query: 106 HNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTDNSRGIRNTRLRQIFK 165
           HNLRNR IK RFQHS  T+H+YFHEVL AM+ FSKEMITPPSF D+S GI N RLRQIFK
Sbjct: 312 HNLRNRLIKNRFQHSSQTIHKYFHEVLVAMVNFSKEMITPPSFNDSSNGISNRRLRQIFK 371

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|147861273|emb|CAN81903.1| hypothetical protein VITISV_041568 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147852015|emb|CAN82284.1| hypothetical protein VITISV_039752 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147792468|emb|CAN74706.1| hypothetical protein VITISV_036360 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147842396|emb|CAN76204.1| hypothetical protein VITISV_020305 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225463187|ref|XP_002267524.1| PREDICTED: putative nuclease HARBI1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|356530983|ref|XP_003534058.1| PREDICTED: uncharacterized protein LOC100811756 [Glycine max] Back     alignment and taxonomy information
>gi|255553963|ref|XP_002518022.1| hypothetical protein RCOM_1176900 [Ricinus communis] gi|223543004|gb|EEF44540.1| hypothetical protein RCOM_1176900 [Ricinus communis] Back     alignment and taxonomy information
>gi|147772236|emb|CAN71557.1| hypothetical protein VITISV_020377 [Vitis vinifera] Back     alignment and taxonomy information
>gi|115474393|ref|NP_001060793.1| Os08g0106900 [Oryza sativa Japonica Group] gi|113622762|dbj|BAF22707.1| Os08g0106900 [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 ?
Query218
TAIR|locus:2165775 374 AT5G41980 [Arabidopsis thalian 0.536 0.312 0.372 1.8e-17
TAIR|locus:2184226 296 AT5G28730 "AT5G28730" [Arabido 0.504 0.371 0.330 5e-11
TAIR|locus:504956234 324 AT1G43722 "AT1G43722" [Arabido 0.399 0.268 0.333 1.2e-05
TAIR|locus:2165775 AT5G41980 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 217 (81.4 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 44/118 (37%), Positives = 73/118 (61%)

Query:    34 TKRQRVSTSSLT-GSLYIQELLNGSPIFCYDLMRMDKNGFISLCQLFKEKGWLSDSKHLT 92
             T  + VS  S++ G+ ++ ++LNG    C++  RMDK  F  LC L + +G L  +  + 
Sbjct:    14 TLPKEVSKISISDGNKFVYQILNGPNEQCFENFRMDKPVFYKLCDLLQTRGLLRHTNRIK 73

Query:    93 VEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMKFSKEMITPPSFTD 150
             +E ++A+FLF I HNLR R ++  F +SG T+ R+F+ VL+A++  SK+   P S +D
Sbjct:    74 IEAQLAIFLFIIGHNLRTRAVQELFCYSGETISRHFNNVLNAVIAISKDFFQPNSNSD 131
GO:0005634 "nucleus" evidence=ISM
GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA
TAIR|locus:2184226 AT5G28730 "AT5G28730" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:504956234 AT1G43722 "AT1G43722" [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:
GSVIVG00032925001
SubName- Full=Chromosome chr14 scaffold_63, whole genome shotgun sequence; (382 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 218
PF1361353 HTH_Tnp_4: Helix-turn-helix of DDE superfamily end 98.78
KOG4585 326 consensus Predicted transposase [Replication, reco 98.67
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 96.19
PF1211682 SpoIIID: Stage III sporulation protein D; InterPro 95.98
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 95.97
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 95.01
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 94.13
COG3415138 Transposase and inactivated derivatives [DNA repli 93.9
smart00351125 PAX Paired Box domain. 93.68
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 93.53
cd00131128 PAX Paired Box domain 93.2
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 93.05
PRK11753211 DNA-binding transcriptional dual regulator Crp; Pr 92.75
PF1351852 HTH_28: Helix-turn-helix domain 92.5
TIGR0253188 yecD_yerC TrpR-related protein YerC/YecD. This mod 92.04
PF0522545 HTH_psq: helix-turn-helix, Psq domain; InterPro: I 91.83
PRK10402226 DNA-binding transcriptional activator YeiL; Provis 91.32
TIGR03697193 NtcA_cyano global nitrogen regulator NtcA, cyanoba 91.28
TIGR0132194 TrpR trp operon repressor, proteobacterial. This m 91.25
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR- 91.1
PRK0138199 Trp operon repressor; Provisional 90.28
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 90.19
PRK04217110 hypothetical protein; Provisional 89.65
cd0657190 Bac_DnaA_C C-terminal domain of bacterial DnaA pro 89.33
PF1354252 HTH_Tnp_ISL3: Helix-turn-helix domain of transposa 88.48
PRK11161235 fumarate/nitrate reduction transcriptional regulat 88.21
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 88.1
PRK09639166 RNA polymerase sigma factor SigX; Provisional 88.03
PRK09391230 fixK transcriptional regulator FixK; Provisional 88.02
cd0009267 HTH_CRP helix_turn_helix, cAMP Regulatory protein 87.28
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 86.84
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 86.69
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 86.65
PRK09392236 ftrB transcriptional activator FtrB; Provisional 86.47
PRK15320251 transcriptional activator SprB; Provisional 86.42
PF0137187 Trp_repressor: Trp repressor protein; InterPro: IP 86.35
PRK00118104 putative DNA-binding protein; Validated 86.08
PRK05911257 RNA polymerase sigma factor sigma-28; Reviewed 85.95
TIGR00721137 tfx DNA-binding protein, Tfx family. Tfx from Meth 85.92
PRK09047161 RNA polymerase factor sigma-70; Validated 85.75
PF0102247 HTH_5: Bacterial regulatory protein, arsR family; 85.18
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 85.12
PRK12529178 RNA polymerase sigma factor; Provisional 85.09
PRK06030124 hypothetical protein; Provisional 85.05
PF1373055 HTH_36: Helix-turn-helix domain 84.93
TIGR02392270 rpoH_proteo alternative sigma factor RpoH. A sigma 84.78
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 84.74
TIGR0284480 spore_III_D sporulation transcriptional regulator 84.51
PRK08301234 sporulation sigma factor SigE; Reviewed 84.25
TIGR02393238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 83.8
PRK07408256 RNA polymerase sigma factor SigF; Reviewed 82.92
PRK12519194 RNA polymerase sigma factor; Provisional 82.76
PRK05803233 sporulation sigma factor SigK; Reviewed 82.11
PF0829970 Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli 82.11
PRK06596284 RNA polymerase factor sigma-32; Reviewed 82.04
PF1301185 LZ_Tnp_IS481: leucine-zipper of insertion element 81.93
PRK09413121 IS2 repressor TnpA; Reviewed 81.63
PRK12524196 RNA polymerase sigma factor; Provisional 81.58
PRK12514179 RNA polymerase sigma factor; Provisional 81.56
PF1284061 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_ 81.13
PRK12532195 RNA polymerase sigma factor; Provisional 80.86
PF0035646 LacI: Bacterial regulatory proteins, lacI family; 80.84
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 80.77
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 80.63
TIGR02997298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 80.4
PF1334075 DUF4096: Putative transposase of IS4/5 family (DUF 80.25
PRK03975141 tfx putative transcriptional regulator; Provisiona 80.16
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease Back     alignment and domain information 
Probab=98.78  E-value=7.3e-09  Score=69.76  Aligned_cols=48  Identities=29%  Similarity=0.451  Sum_probs=45.9

Q ss_pred             cchHHHHHHHHHHHHhcCccchhhhhcccccccchhHHHHHHHHHHHh
Q 046385           90 HLTVEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFHEVLSAMMK  137 (218)
Q Consensus        90 ~isveE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~eVl~AI~~  137 (218)
                      .+|.++|+.++|.++.+|.++.+++.+||+|.+||||+|+++++.+..
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~   49 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ   49 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999999999874

>KOG4585 consensus Predicted transposase [Replication, recombination and repair] Back     alignment and domain information
>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
>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
>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
>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
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00351 PAX Paired Box domain Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>cd00131 PAX Paired Box domain Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional Back     alignment and domain information
>PF13518 HTH_28: Helix-turn-helix domain Back     alignment and domain information
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD 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
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional Back     alignment and domain information
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial Back     alignment and domain information
>TIGR01321 TrpR trp operon repressor, proteobacterial Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>PRK01381 Trp operon repressor; Provisional Back     alignment and domain information
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs) Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins Back     alignment and domain information
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3 Back     alignment and domain information
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK09391 fixK transcriptional regulator FixK; Provisional 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
>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
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>PRK09392 ftrB transcriptional activator FtrB; Provisional Back     alignment and domain information
>PRK15320 transcriptional activator SprB; Provisional 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
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>TIGR00721 tfx DNA-binding protein, Tfx family Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated 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
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06030 hypothetical protein; Provisional Back     alignment and domain information
>PF13730 HTH_36: Helix-turn-helix domain Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH 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
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID Back     alignment and domain information
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed 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
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481 Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional 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
>PRK12532 RNA polymerase sigma factor; 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
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096) Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional 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 ?
Query218
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-05
>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 = 44.8 bits (105), Expect = 1e-05
 Identities = 34/221 (15%), Positives = 76/221 (34%), Gaps = 69/221 (31%)

Query: 1   MAMADEEVDIKIGVRRILRKQLI-----MLVKKLLKGS--TKRQRVSTSSLTGSLYIQEL 53
           +++      I   +  ++   +I     ++V KL K S   K+ + ST S+   +Y++  
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS-IYLELK 436

Query: 54  --------LNGSPIFCYDLMR-MDKNGFISLCQ---LFKEKGWLSDSKHLTV---EEKMA 98
                   L+ S +  Y++ +  D +  I        +   G      HL      E+M 
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH-----HLKNIEHPERMT 491

Query: 99  MF--LFTISHNLRNRFIKIRFQHSG----------HTV-------------HRYFHEVLS 133
           +F  +F    + R  F++ + +H            +T+                +  +++
Sbjct: 492 LFRMVFL---DFR--FLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVN 546

Query: 134 AMMKF----------SKEM-ITPPSFTDNSRGIRNTRLRQI 163
           A++ F          SK   +   +       I     +Q+
Sbjct: 547 AILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query218
1jhg_A101 Trp operon repressor; complex (regulatory protein- 95.81
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 94.85
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 93.63
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 93.24
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 92.87
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 92.86
2w7n_A101 TRFB transcriptional repressor protein; INCP, plas 92.6
3frw_A107 Putative Trp repressor protein; structural genomic 92.53
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 92.42
2jpc_A61 SSRB; DNA binding protein, structural genomics, PS 91.85
3c57_A95 Two component transcriptional regulatory protein; 91.78
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 91.67
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 91.64
2fmy_A220 COOA, carbon monoxide oxidation system transcripti 91.46
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 91.29
1o5l_A213 Transcriptional regulator, CRP family; TM1171, str 90.99
3t72_q99 RNA polymerase sigma factor RPOD, DNA-directed RN 90.99
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 90.83
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 90.77
3ryp_A210 Catabolite gene activator; CAMP receptor protein ( 90.73
3dv8_A220 Transcriptional regulator, CRP/FNR family; cyclic 90.61
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 90.22
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type dom 90.21
1ft9_A222 Carbon monoxide oxidation system transcription reg 90.12
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 90.01
3la7_A243 Global nitrogen regulator; activator, DNA-binding, 89.56
2oz6_A207 Virulence factor regulator; winged helix, helix-tu 89.53
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 89.44
1iuf_A144 Centromere ABP1 protein; riken structural genomics 89.4
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 89.2
1zyb_A232 Transcription regulator, CRP family; NP_813211.1, 89.2
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 88.92
3dkw_A227 DNR protein; CRP-FNR, HTH, beta barrel, dimerizati 88.8
4ev0_A216 Transcription regulator, CRP family; CAMP binding, 88.64
3iwz_A230 CAP-like, catabolite activation-like protein; XCC, 88.37
1u78_A141 TC3 transposase, transposable element TC3 transpos 88.29
3fx3_A237 Cyclic nucleotide-binding protein; helix_TURN_heli 88.23
3e6c_C250 CPRK, cyclic nucleotide-binding protein; CPRK, hal 88.1
3kcc_A260 Catabolite gene activator; helix-turn-helix, CAMP, 87.55
2jrt_A95 Uncharacterized protein; solution, structure, NESG 87.51
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 87.35
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 86.95
1u78_A141 TC3 transposase, transposable element TC3 transpos 86.77
1j1v_A94 Chromosomal replication initiator protein DNAA, 5' 86.76
2bgc_A238 PRFA; bacterial infection, human pathogen, transcr 86.44
3d0s_A227 Transcriptional regulatory protein; CAMP receptor 86.2
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 86.04
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP 86.01
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 85.45
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 85.45
3e97_A231 Transcriptional regulator, CRP/FNR family; YP_6044 85.44
2jt1_A77 PEFI protein; solution structure, winged helix-tur 85.34
2gau_A232 Transcriptional regulator, CRP/FNR family; structu 84.98
2k27_A159 Paired box protein PAX-8; paired domain, solution 84.63
2lkp_A119 Transcriptional regulator, ARSR family; symmetric 83.68
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-h 83.59
3b02_A195 Transcriptional regulator, CRP family; structural 81.67
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 81.66
1wy3_A35 Villin; structural protein; HET: NLE; 0.95A {Synth 81.18
2zcw_A202 TTHA1359, transcriptional regulator, FNR/CRP famil 81.0
3dn7_A194 Cyclic nucleotide binding regulatory protein; stru 80.59
3szt_A237 QCSR, quorum-sensing control repressor; quorum sen 80.53
3pvv_A101 Chromosomal replication initiator protein DNAA; he 80.27
3kor_A119 Possible Trp repressor; putative DNA-binding Trp r 80.18
1r1u_A106 CZRA, repressor protein; zinc, DNA binding, transc 80.1
>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
Probab=95.81  E-value=0.0034  Score=46.80  Aligned_cols=46  Identities=22%  Similarity=0.145  Sum_probs=36.5

Q ss_pred             cchHHHHHHHHHHH-----HhcC-ccchhhhhcccccccchhHHHHHHHHHHH
Q 046385           90 HLTVEEKMAMFLFT-----ISHN-LRNRFIKIRFQHSGHTVHRYFHEVLSAMM  136 (218)
Q Consensus        90 ~isveE~laifL~~-----la~~-~s~r~i~~~F~~S~sTVsr~f~eVl~AI~  136 (218)
                      -+++.|+-+|.+++     |..| .+||.|+...|+|.+||||+ ...++-+.
T Consensus        35 lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~   86 (101)
T 1jhg_A           35 MLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAP   86 (101)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSC
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHcc
Confidence            36788887777764     2356 99999999999999999999 66665543
>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
>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
>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
>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
>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
>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli} 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
>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
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium} 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
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} 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
>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
>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
>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
>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
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} 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
>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
>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
>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
>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
>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
>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
>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
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} 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
>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
>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
>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
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa} 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
>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
>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
>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
>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
>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
>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides} 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
>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
>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
>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
>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
>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
>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
>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
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} 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
>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
>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
>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
>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
>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis} 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
>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
>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
>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus} 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
>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
>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
>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus} 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

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 ?
Query218
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 96.52
d1hlva166 DNA-binding domain of centromere binding protein B 94.67
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 93.24
d1i5za169 Catabolite gene activator protein (CAP), C-termina 92.43
d1k78a163 Pax-5 {Human (Homo sapiens) [TaxId: 9606]} 91.61
d1ft9a180 CO-sensing protein CooA, C-terminal domain {Rhodos 91.36
d1pdnc_123 Paired protein (prd) {Fruit fly (Drosophila melano 90.2
d1l3la165 Quorum-sensing transcription factor TraR, C-termin 89.79
d2gaua181 Transcriptional regulator PG0396, C-terminal domai 89.79
d1zyba173 Probable transcription regulator BT4300, C-termina 89.61
d3e5ua180 Chlorophenol reduction protein CprK {Desulfitobact 89.54
d1a04a167 Nitrate/nitrite response regulator (NarL) {Escheri 89.04
d1yioa170 Response regulatory protein StyR, C-terminal domai 87.18
d1p4wa_87 Transcriptional regulator RcsB {Erwinia amylovora 87.12
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 86.51
d1ku3a_61 Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27 85.43
d2zcwa182 Transcriptional regulator TTHA1359, C-terminal dom 84.38
d1r1ua_94 Metal-sensing transcriptional repressor CzrA {Stap 83.7
d1s7oa_106 Hypothetical protein SPy1201 {Streptococcus pyogen 83.32
d1r1ta_98 SmtB repressor {Cyanobacteria (Synechococcus), pcc 83.19
d1aisb198 Transcription factor IIB (TFIIB), core domain {Arc 82.28
d1qpza157 Purine repressor (PurR), N-terminal domain {Escher 81.95
d1vola2109 Transcription factor IIB (TFIIB), core domain {Hum 80.68
d1jhga_101 Trp repressor, TrpR {Escherichia coli [TaxId: 562] 80.07
>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=96.52  E-value=0.00048  Score=42.88  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHhcCccchhhhhcccccccchhHHHH
Q 046385           93 VEEKMAMFLFTISHNLRNRFIKIRFQHSGHTVHRYFH  129 (218)
Q Consensus        93 veE~laifL~~la~~~s~r~i~~~F~~S~sTVsr~f~  129 (218)
                      .+||+.-....++.|.+..+|+..||+|++||+|+|.
T Consensus         7 t~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           7 NKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhCC
Confidence            3578889999999999999999999999999999973
>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
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>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
>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {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
>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]} 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
>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]} 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
>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Back     information, alignment and structure
>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]} Back     information, alignment and structure
>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} 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
>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]} Back     information, alignment and structure
>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]} 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
>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vola2 a.74.1.2 (A:208-316) Transcription factor IIB (TFIIB), core domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]} Back     information, alignment and structure