Citrus Sinensis ID: 025268

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-------220-------230-------240-------250-----
MGSETFDHFHEDKTSTKRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQENEETSHAVEAEAPVSEQSKNHVSSENANAQLLTSPPSFSPLFTGSSSSSHPSMNWVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFTGH
cccccccccccccccccccccccccHHHHHccccccccHHHHcccccccccccHHHHHHHHHHcHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccccccccccccccccccccccccccccccccccccHHHHHcccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccEEEcccccccccccccccccccccccccccccccc
mgsetfdhfhedktstkrKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFevdnklepdRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQEneetshaveaeapvseqsknhvssenanaqlltsppsfsplftgssssshpsmnwvqfsdsrtilsnvyqqpqlvkVEEQsllfnpedpcnifsvdqaptlqwyftgh
mgsetfdhfhedktstkrkqiyGREFQAMMDCLEEEDCREEASQatekkrrltvdqvkaleknfevdnklepdrKVKLaeelglqprqiavwfqnrRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQENEETShaveaeapvseqskNHVSSENANAQLLTSPPSFSPLFTGSSSSSHPSMNWVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFTGH
MGSETFDHFHEDKTSTKRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQENEETSHAVEAEAPVSEQSKNHVSSENANAQLltsppsfsplftgssssshpsMNWVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFTGH
*******************************************************************************EELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQ**************************************************************************WVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFT**
*******************************************************QVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRA*************************************************************************************************************************************NPEDPCNIFSVDQAPTLQWYFT**
****************KRKQIYGREFQAMMDCLE*****************LTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKLCQ***************************ANAQLLTSPPSFSP***********SMNWVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFTGH
**********************************************EKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELRELKAKL**************************************************************D***ILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYF***
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGSETFDHFHEDKTSTKRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTSHAVEAEAPVSEQSKNHVSSENANAQLLTSPPSFSPLFTGSSSSSHPSMNWVQFSDSRTILSNVYQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFTGH
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 ?
Query255 2.2.26 [Sep-21-2011]
P46668311 Homeobox-leucine zipper p yes no 0.890 0.729 0.374 8e-41
P46667312 Homeobox-leucine zipper p no no 0.941 0.769 0.377 6e-40
Q940J1294 Homeobox-leucine zipper p no no 0.901 0.782 0.385 5e-39
Q6Z248269 Homeobox-leucine zipper p yes no 0.831 0.788 0.391 3e-35
A2YWC0269 Homeobox-leucine zipper p N/A no 0.831 0.788 0.391 3e-35
Q6K498277 Homeobox-leucine zipper p no no 0.501 0.462 0.564 9e-35
Q9XH37277 Homeobox-leucine zipper p N/A no 0.501 0.462 0.564 9e-35
Q8LC03294 Homeobox-leucine zipper p no no 0.611 0.530 0.493 4e-34
Q10QP3311 Homeobox-leucine zipper p no no 0.439 0.360 0.571 5e-33
A2XDD6312 Homeobox-leucine zipper p N/A no 0.439 0.358 0.566 1e-31
>sp|P46668|ATHB6_ARATH Homeobox-leucine zipper protein ATHB-6 OS=Arabidopsis thaliana GN=ATHB-6 PE=1 SV=1 Back     alignment and function desciption
 Score =  167 bits (422), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 104/278 (37%), Positives = 151/278 (54%), Gaps = 51/278 (18%)

Query: 23  GREFQAMMDCLEEEDCREEASQA----TEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKL 78
           GREFQ+M++  EEE+      +     +EKKRRL+++QVKALEKNFE++NKLEP+RKVKL
Sbjct: 33  GREFQSMLEGYEEEEEAIVEERGHVGLSEKKRRLSINQVKALEKNFELENKLEPERKVKL 92

Query: 79  AEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAELR 138
           A+ELGLQPRQ+AVWFQNRRAR K+K+LE+DYG+LK  YD+LR ++++L+++NE+L  E+ 
Sbjct: 93  AQELGLQPRQVAVWFQNRRARWKTKQLEKDYGVLKTQYDSLRHNFDSLRRDNESLLQEIS 152

Query: 139 ELKAKLCQENEETSHAVEAEAPVSEQSKNHVSSENANAQLLTSPPSFSPLFTGSSSSSHP 198
           +LK KL     E        A  +E   +    E +  + +T  PS  P F   S     
Sbjct: 153 KLKTKLNGGGGEEEEEENNAAVTTESDISVKEEEVSLPEKITEAPSSPPQFLEHSDG--- 209

Query: 199 SMNWVQFSDSRTIL-------------------------------------------SNV 215
            +N+  F+D R +L                                            N 
Sbjct: 210 -LNYRSFTDLRDLLPLKAAASSFAAAAGSSDSSDSSALLNEESSSNVTVAAPVTVPGGNF 268

Query: 216 YQQPQLVKVEEQSLLFNPEDPCNIFSVDQAPTLQWYFT 253
           +Q  ++ + E+     + E+ C  FS +Q P+L WY T
Sbjct: 269 FQFVKMEQTEDHEDFLSGEEACEFFSDEQPPSLHWYST 306
Transcription activator that may act as growth regulators in response to water deficit. Interacts with the core sequence 5'-CAATTATTA-3' of promoters in response to ABA and in an ABI1-dependent manner. Involved in the negative regulation of the ABA signaling pathway.
Arabidopsis thaliana (taxid: 3702)
>sp|P46667|ATHB5_ARATH Homeobox-leucine zipper protein ATHB-5 OS=Arabidopsis thaliana GN=ATHB-5 PE=1 SV=1 Back     alignment and function description
>sp|Q940J1|ATB16_ARATH Homeobox-leucine zipper protein ATHB-16 OS=Arabidopsis thaliana GN=ATHB-16 PE=2 SV=2 Back     alignment and function description
>sp|Q6Z248|HOX20_ORYSJ Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. japonica GN=HOX20 PE=2 SV=1 Back     alignment and function description
>sp|A2YWC0|HOX20_ORYSI Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. indica GN=HOX20 PE=2 SV=1 Back     alignment and function description
>sp|Q6K498|HOX4_ORYSJ Homeobox-leucine zipper protein HOX4 OS=Oryza sativa subsp. japonica GN=HOX4 PE=1 SV=1 Back     alignment and function description
>sp|Q9XH37|HOX4_ORYSI Homeobox-leucine zipper protein HOX4 OS=Oryza sativa subsp. indica GN=HOX4 PE=1 SV=1 Back     alignment and function description
>sp|Q8LC03|ATB13_ARATH Homeobox-leucine zipper protein ATHB-13 OS=Arabidopsis thaliana GN=ATHB-13 PE=2 SV=2 Back     alignment and function description
>sp|Q10QP3|HOX13_ORYSJ Homeobox-leucine zipper protein HOX13 OS=Oryza sativa subsp. japonica GN=HOX13 PE=2 SV=1 Back     alignment and function description
>sp|A2XDD6|HOX13_ORYSI Homeobox-leucine zipper protein HOX13 OS=Oryza sativa subsp. indica GN=HOX13 PE=2 SV=2 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 ?
Query255
224066989265 predicted protein [Populus trichocarpa] 0.905 0.871 0.596 2e-70
255545820268 homeobox protein, putative [Ricinus comm 0.925 0.880 0.600 4e-70
224082070250 predicted protein [Populus trichocarpa] 0.882 0.9 0.581 5e-65
225459213287 PREDICTED: homeobox-leucine zipper prote 0.890 0.790 0.518 3e-63
302141999312 unnamed protein product [Vitis vinifera] 0.901 0.737 0.523 9e-62
297741835280 unnamed protein product [Vitis vinifera] 0.937 0.853 0.494 5e-56
357462199255 Homeobox-leucine zipper-like protein [Me 0.870 0.870 0.543 3e-55
302398839274 HD domain class transcription factor [Ma 0.878 0.817 0.487 1e-54
356540251314 PREDICTED: homeobox-leucine zipper prote 0.890 0.722 0.446 6e-53
356567620322 PREDICTED: homeobox-leucine zipper prote 0.917 0.726 0.438 1e-52
>gi|224066989|ref|XP_002302314.1| predicted protein [Populus trichocarpa] gi|222844040|gb|EEE81587.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 148/248 (59%), Positives = 178/248 (71%), Gaps = 17/248 (6%)

Query: 17  KRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKV 76
           K  Q Y R+FQ+M+D LEEED  E AS   EKKRRL + QVKALEKNFEV+NKLEP+RK+
Sbjct: 26  KTNQGYSRDFQSMLDSLEEEDYSEAASHVGEKKRRLNLHQVKALEKNFEVENKLEPERKL 85

Query: 77  KLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQQENEALTAE 136
           KLA ELGLQPRQ+A+WFQNRRAR K+K+LERDYG LKANY+AL+LDY NL+Q+NE L  +
Sbjct: 86  KLAGELGLQPRQVAIWFQNRRARWKTKQLERDYGTLKANYEALKLDYCNLEQKNEVLAQK 145

Query: 137 LRELKAKLCQENEETSHAVEAEAPVSE-------QSKNHVSSENANAQLLTSPPSFSPLF 189
           ++ELKAKL +EN ++SH+V+ E  VSE        SKN   SE  N+  +T   S     
Sbjct: 146 VKELKAKLSEENVDSSHSVKEEHRVSESDNNASVHSKNRDFSEKNNSSAITKDHS----- 200

Query: 190 TGSSSSSHPSMNWVQFSDSRTILSNVYQ--QPQLVKVEEQSLLFNPEDPCNIFSVDQAPT 247
             + SSSH  MN  Q SDSR IL N+YQ  QP L+K EEQS LF+ E+ CN FSVDQAPT
Sbjct: 201 --NISSSHELMNLFQLSDSRVILGNIYQVYQPHLMKPEEQS-LFSTEESCNFFSVDQAPT 257

Query: 248 LQWYFTGH 255
           L  YF  H
Sbjct: 258 LHCYFPEH 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255545820|ref|XP_002513970.1| homeobox protein, putative [Ricinus communis] gi|223547056|gb|EEF48553.1| homeobox protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224082070|ref|XP_002306561.1| predicted protein [Populus trichocarpa] gi|222856010|gb|EEE93557.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225459213|ref|XP_002285743.1| PREDICTED: homeobox-leucine zipper protein ATHB-16-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|302141999|emb|CBI19202.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|297741835|emb|CBI33148.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|357462199|ref|XP_003601381.1| Homeobox-leucine zipper-like protein [Medicago truncatula] gi|355490429|gb|AES71632.1| Homeobox-leucine zipper-like protein [Medicago truncatula] Back     alignment and taxonomy information
>gi|302398839|gb|ADL36714.1| HD domain class transcription factor [Malus x domestica] Back     alignment and taxonomy information
>gi|356540251|ref|XP_003538603.1| PREDICTED: homeobox-leucine zipper protein ATHB-6-like [Glycine max] Back     alignment and taxonomy information
>gi|356567620|ref|XP_003552015.1| PREDICTED: homeobox-leucine zipper protein ATHB-6-like [Glycine max] 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 ?
Query255
TAIR|locus:2041283311 HB6 "homeobox protein 6" [Arab 0.584 0.479 0.55 1e-47
TAIR|locus:2168225312 HB5 "homeobox protein 5" [Arab 0.568 0.464 0.551 6.7e-43
TAIR|locus:2140055294 HB16 "homeobox protein 16" [Ar 0.584 0.506 0.503 2.8e-40
TAIR|locus:2205075294 ATHB13 [Arabidopsis thaliana ( 0.529 0.459 0.525 9.8e-32
TAIR|locus:2084228272 HB-1 "homeobox 1" [Arabidopsis 0.541 0.507 0.496 6.9e-31
TAIR|locus:2102107286 HB20 "homeobox protein 20" [Ar 0.541 0.482 0.485 2.1e-29
TAIR|locus:2202795255 AtHB23 "homeobox protein 23" [ 0.533 0.533 0.478 2.7e-29
TAIR|locus:2150901314 HB-3 "homeobox 3" [Arabidopsis 0.541 0.439 0.472 3.1e-28
TAIR|locus:2062754258 HB-7 "homeobox 7" [Arabidopsis 0.525 0.519 0.425 1.9e-26
TAIR|locus:2079542235 HB-12 "homeobox 12" [Arabidops 0.521 0.565 0.370 3.8e-23
TAIR|locus:2041283 HB6 "homeobox protein 6" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 417 (151.9 bits), Expect = 1.0e-47, Sum P(3) = 1.0e-47
 Identities = 88/160 (55%), Positives = 122/160 (76%)

Query:    12 DKTSTKRKQIYGREFQAMMDCLEEED--CREEASQA--TEKKRRLTVDQVKALEKNFEVD 67
             D+ S +R    GREFQ+M++  EEE+    EE      +EKKRRL+++QVKALEKNFE++
Sbjct:    24 DEQSPRRYG--GREFQSMLEGYEEEEEAIVEERGHVGLSEKKRRLSINQVKALEKNFELE 81

Query:    68 NKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLDYNNLQ 127
             NKLEP+RKVKLA+ELGLQPRQ+AVWFQNRRAR K+K+LE+DYG+LK  YD+LR ++++L+
Sbjct:    82 NKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLEKDYGVLKTQYDSLRHNFDSLR 141

Query:   128 QENEALTAELRELKAKLC-----QENEETSHAVEAEAPVS 162
             ++NE+L  E+ +LK KL      +E EE + AV  E+ +S
Sbjct:   142 RDNESLLQEISKLKTKLNGGGGEEEEEENNAAVTTESDIS 181
GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA;IDA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS;TAS
GO:0005634 "nucleus" evidence=ISM;IEA;ISS;IDA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS
GO:0043565 "sequence-specific DNA binding" evidence=IEA;IDA
GO:0009414 "response to water deprivation" evidence=IEP
GO:0005515 "protein binding" evidence=IPI
GO:0009738 "abscisic acid mediated signaling pathway" evidence=TAS
GO:0009788 "negative regulation of abscisic acid mediated signaling pathway" evidence=IMP
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA
GO:0009269 "response to desiccation" evidence=RCA
GO:0009409 "response to cold" evidence=RCA
GO:0009651 "response to salt stress" evidence=RCA
GO:0009737 "response to abscisic acid stimulus" evidence=RCA
GO:0042744 "hydrogen peroxide catabolic process" evidence=RCA
TAIR|locus:2168225 HB5 "homeobox protein 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2140055 HB16 "homeobox protein 16" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2205075 ATHB13 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2084228 HB-1 "homeobox 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2102107 HB20 "homeobox protein 20" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2202795 AtHB23 "homeobox protein 23" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2150901 HB-3 "homeobox 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2062754 HB-7 "homeobox 7" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2079542 HB-12 "homeobox 12" [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

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 ?
Query255
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 5e-15
pfam0004657 pfam00046, Homeobox, Homeobox domain 6e-15
smart0038957 smart00389, HOX, Homeodomain 9e-15
pfam0218345 pfam02183, HALZ, Homeobox associated leucine zippe 2e-11
COG5576156 COG5576, COG5576, Homeodomain-containing transcrip 5e-10
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information 
 Score = 67.3 bits (165), Expect = 5e-15
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query: 48  KKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKE 104
           K+ R T +Q++ LEK FE +     + + +LA+ELGL  RQ+ +WFQNRRA+LK  E
Sbjct: 3   KRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRSE 59

Length = 59
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|202143 pfam02183, HALZ, Homeobox associated leucine zipper Back     alignment and domain information
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 255
KOG0483198 consensus Transcription factor HEX, contains HOX a 99.88
KOG4577383 consensus Transcription factor LIM3, contains LIM 99.74
KOG0489261 consensus Transcription factor zerknullt and relat 99.74
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.63
KOG0488309 consensus Transcription factor BarH and related HO 99.61
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.59
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.58
KOG0843197 consensus Transcription factor EMX1 and related HO 99.56
KOG0848317 consensus Transcription factor Caudal, contains HO 99.54
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.53
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.53
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.51
KOG2251228 consensus Homeobox transcription factor [Transcrip 99.5
KOG0850245 consensus Transcription factor DLX and related pro 99.48
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.45
COG5576156 Homeodomain-containing transcription factor [Trans 99.45
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.43
KOG0494332 consensus Transcription factor CHX10 and related H 99.43
KOG3802398 consensus Transcription factor OCT-1, contains POU 99.41
KOG0493342 consensus Transcription factor Engrailed, contains 99.4
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.33
KOG0844408 consensus Transcription factor EVX1, contains HOX 99.26
KOG0491194 consensus Transcription factor BSH, contains HOX d 99.2
KOG0847288 consensus Transcription factor, contains HOX domai 99.14
KOG0486351 consensus Transcription factor PTX1, contains HOX 99.08
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 99.01
KOG0490235 consensus Transcription factor, contains HOX domai 98.92
KOG0849354 consensus Transcription factor PRD and related pro 98.69
KOG0775304 consensus Transcription factor SIX and related HOX 98.68
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.23
PF0218345 HALZ: Homeobox associated leucine zipper; InterPro 98.15
KOG0774334 consensus Transcription factor PBX and related HOX 98.1
KOG2252558 consensus CCAAT displacement protein and related h 97.88
KOG0490235 consensus Transcription factor, contains HOX domai 97.66
KOG1146 1406 consensus Homeobox protein [General function predi 97.07
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 96.04
KOG0773342 consensus Transcription factor MEIS1 and related H 95.3
PF0218345 HALZ: Homeobox associated leucine zipper; InterPro 94.06
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 93.88
PRK09413121 IS2 repressor TnpA; Reviewed 93.4
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 92.26
smart0034044 HALZ homeobox associated leucin zipper. 89.99
KOG4196135 consensus bZIP transcription factor MafK [Transcri 88.52
KOG4005292 consensus Transcription factor XBP-1 [Transcriptio 87.1
PF0017064 bZIP_1: bZIP transcription factor cAMP response el 86.45
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information 
Probab=99.88  E-value=2.2e-22  Score=174.70  Aligned_cols=105  Identities=58%  Similarity=0.859  Sum_probs=99.7

Q ss_pred             ccCCCCCCcCCHHHHHHHHHHhHhcCCCCHHHHHHHHHHhCCCcchhhhhhhhhHHHhhHHHHHHHHhHHHHhHHHHHHH
Q 025268           43 SQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLKSKELERDYGLLKANYDALRLD  122 (255)
Q Consensus        43 ~~~~~kr~r~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kkk~~~~~~~~lk~~~~~l~~~  122 (255)
                      ....+|++||+.+|+..||..|+...++.+.++..||++|||.+|||+|||||||||||.++++.+|+.|+..++.|+.+
T Consensus        48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~  127 (198)
T KOG0483|consen   48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSE  127 (198)
T ss_pred             cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhh
Confidence            34677889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhh
Q 025268          123 YNNLQQENEALTAELRELKAKLCQE  147 (255)
Q Consensus       123 ~~~l~~en~~l~~e~~~l~~~l~~~  147 (255)
                      +..|+.++..|.+++..++..++..
T Consensus       128 ~~~Lq~e~~eL~~~~~~~~~~~~~~  152 (198)
T KOG0483|consen  128 NDRLQSEVQELVAELSSLKREMQKS  152 (198)
T ss_pred             hhHHHHHHHHHHHHHhhhhhhhccC
Confidence            9999999999999999988888754

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription] Back     alignment and domain information
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [] Back     alignment and domain information
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox [] Back     alignment and domain information
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox [] Back     alignment and domain information
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription] Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed 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
>smart00340 HALZ homeobox associated leucin zipper Back     alignment and domain information
>KOG4196 consensus bZIP transcription factor MafK [Transcription] Back     alignment and domain information
>KOG4005 consensus Transcription factor XBP-1 [Transcription] Back     alignment and domain information
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query255
2e1o_A70 Solution Structure Of Rsgi Ruh-028, A Homeobox Doma 1e-05
1puf_A77 Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo 1e-04
9ant_A62 Antennapedia Homeodomain-Dna Complex Length = 62 1e-04
2dmt_A80 Solution Structure Of The Homeobox Domain Of Homeob 1e-04
1b72_A97 Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le 1e-04
1san_A62 The Des(1-6)antennapedia Homeodomain: Comparison Of 1e-04
1b8i_A81 Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX 2e-04
2r5y_A88 Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HO 2e-04
1ahd_P68 Determination Of The Nmr Solution Structure Of An A 2e-04
2lp0_A60 The Solution Structure Of Homeodomain-Protein Compl 3e-04
3hdd_A60 Engrailed Homeodomain Dna Complex Length = 60 4e-04
1ftz_A70 Nuclear Magnetic Resonance Solution Structure Of Th 4e-04
1hdd_C61 Crystal Structure Of An Engrailed Homeodomain-Dna C 4e-04
2h1k_A63 Crystal Structure Of The Pdx1 Homeodomain In Comple 7e-04
2l9r_A69 Solution Nmr Structure Of Homeobox Domain Of Homeob 7e-04
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna Length = 70 Back     alignment and structure 
Iteration: 1

 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 30/51 (58%)
Query: 51  RLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
           R + DQ   LEK FE    L P  + +LA+ L L  RQ+  WFQNRRA+ +
Sbjct: 13  RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 77 Back     alignment and structure
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex Length = 62 Back     alignment and structure
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80 Back     alignment and structure
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 97 Back     alignment and structure
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The Nmr Solution Structure And The Dna Binding Affinity With The Intact Antennapedia Homeodomain Length = 62 Back     alignment and structure
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 81 Back     alignment and structure
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd Site Length = 88 Back     alignment and structure
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An Antennapedia Homeodomain-Dna Complex Length = 68 Back     alignment and structure
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex Length = 60 Back     alignment and structure
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60 Back     alignment and structure
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi Tarazu Homeodomain From Drosophila And Comparison With The Antennapedia Homeodomain Length = 70 Back     alignment and structure
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61 Back     alignment and structure
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With Dna Length = 63 Back     alignment and structure
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query255
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 7e-25
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 6e-14
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 7e-14
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 1e-12
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 1e-12
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-12
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 2e-12
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 1e-11
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 1e-11
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 1e-11
2xsd_C164 POU domain, class 3, transcription factor 1; trans 8e-11
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 2e-10
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 2e-10
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 2e-10
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 6e-10
1e3o_C160 Octamer-binding transcription factor 1; transcript 6e-10
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 6e-10
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 7e-10
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 8e-10
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 1e-09
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 1e-09
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-09
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 2e-09
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 3e-09
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 4e-09
3d1n_I151 POU domain, class 6, transcription factor 1; prote 4e-09
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 4e-09
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 5e-09
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 5e-09
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 6e-09
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 8e-09
3a01_A93 Homeodomain-containing protein; homeodomain, prote 1e-08
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 2e-08
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 3e-08
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 3e-08
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 3e-08
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 6e-08
1uhs_A72 HOP, homeodomain only protein; structural genomics 7e-08
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 7e-08
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 9e-08
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 1e-07
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 1e-07
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 1e-07
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 2e-07
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 3e-07
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 9e-07
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 9e-07
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 5e-06
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 1e-05
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 2e-05
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 4e-05
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 5e-05
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 5e-05
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 6e-05
3a02_A60 Homeobox protein aristaless; homeodomain, developm 7e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 1e-04
2e19_A64 Transcription factor 8; homeobox domain, structura 1e-04
2dfs_A1080 Myosin-5A; myosin-V, inhibited state, cryoelectron 1e-04
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 3e-04
1i84_S1184 Smooth muscle myosin heavy chain; muscle protein, 4e-04
1i84_S1184 Smooth muscle myosin heavy chain; muscle protein, 4e-04
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 5e-04
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 7e-04
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61 Back     alignment and structure
 Score = 92.6 bits (231), Expect = 7e-25
 Identities = 17/61 (27%), Positives = 31/61 (50%)

Query: 41  EASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARL 100
           +  ++ + K  ++      LE+ F     L    K ++A++ G+ P Q+ VWF N+R R 
Sbjct: 1   KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60

Query: 101 K 101
           K
Sbjct: 61  K 61
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76 Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75 Back     alignment and structure
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146 Back     alignment and structure
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89 Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89 Back     alignment and structure
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 Back     alignment and structure
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66 Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71 Back     alignment and structure
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69 Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160 Back     alignment and structure
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66 Back     alignment and structure
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155 Back     alignment and structure
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61 Back     alignment and structure
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62 Back     alignment and structure
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151 Back     alignment and structure
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84 Back     alignment and structure
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77 Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58 Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93 Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60 Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81 Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88 Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63 Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73 Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68 Back     alignment and structure
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97 Back     alignment and structure
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77 Back     alignment and structure
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96 Back     alignment and structure
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76 Back     alignment and structure
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64 Back     alignment and structure
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80 Back     alignment and structure
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Length = 81 Back     alignment and structure
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67 Back     alignment and structure
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80 Back     alignment and structure
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68 Back     alignment and structure
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Length = 60 Back     alignment and structure
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60 Back     alignment and structure
>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
>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64 Back     alignment and structure
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp contractIle protein-transport protein complex; 24.00A {Gallus gallus} Length = 1080 Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Length = 87 Back     alignment and structure
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184 Back     alignment and structure
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin subfragment 2, heavy meromyosin, essential light chain, motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP: i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A Length = 1184 Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64 Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Length = 83 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query255
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.8
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.79
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.74
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.74
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.74
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.74
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.73
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.73
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.73
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.73
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.73
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.73
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.72
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.72
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.72
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.72
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.72
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.72
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.72
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.72
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.72
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.71
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.71
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.71
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.71
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.71
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.71
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.71
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.7
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.7
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.7
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.7
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.7
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.7
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.7
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.7
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.7
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.69
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.69
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.69
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.69
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.68
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.68
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.67
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.67
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.67
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.67
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.67
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.67
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.66
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.66
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.66
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.64
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.64
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.64
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.64
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.63
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.63
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.62
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.62
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.62
2e19_A64 Transcription factor 8; homeobox domain, structura 99.62
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.61
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.6
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.6
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.58
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.58
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.58
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.56
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.55
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.54
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.53
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.38
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.34
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.29
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.2
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.15
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.86
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 93.28
2yy0_A53 C-MYC-binding protein; conserved hypothetical prot 88.84
2wt7_B90 Transcription factor MAFB; transcription, transcri 86.32
1hjb_A87 Ccaat/enhancer binding protein beta; transcription 84.89
2wt7_A63 Proto-oncogene protein C-FOS; transcription, trans 83.82
1ci6_A63 Transcription factor ATF-4; BZIP; 2.60A {Homo sapi 83.22
1t2k_D61 Cyclic-AMP-dependent transcription factor ATF-2; p 82.36
1gu4_A78 CAAT/enhancer binding protein beta; transcription/ 82.11
1gd2_E70 Transcription factor PAP1; basic leucine zipper, p 81.79
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
Probab=99.80  E-value=6.6e-20  Score=141.27  Aligned_cols=87  Identities=29%  Similarity=0.489  Sum_probs=63.3

Q ss_pred             CCCcCCCCcccccccccccccCcchhhhhcccchhhhhhhhccCCCCCCcCCHHHHHHHHHHhHhcCCCCHHHHHHHHHH
Q 025268            2 GSETFDHFHEDKTSTKRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEE   81 (255)
Q Consensus         2 g~q~~~w~~e~~~~~~~~~~~~~e~~~m~~~~~~~~~~~~~~~~~~kr~r~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~   81 (255)
                      +.+||+||++.+..++..  ...              ....+..+++|++||..|+.+||..|..++||+..++..||..
T Consensus         7 ~~~~~~W~~~~r~~~~~~--~~~--------------~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~   70 (97)
T 1b72_A            7 TARTFDWMKVKRNPPKTA--KVS--------------EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAAT   70 (97)
T ss_dssp             -CCCCGGGGC------------------------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             CcccccccccccCCCCCC--CCC--------------CCCCCCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHH
Confidence            468999999988433321  000              0112345667788999999999999999999999999999999


Q ss_pred             hCCCcchhhhhhhhhHHHhhHHH
Q 025268           82 LGLQPRQIAVWFQNRRARLKSKE  104 (255)
Q Consensus        82 LgL~~rqVqvWFQNRRak~Kkk~  104 (255)
                      |||+++||+|||||||+|+|+..
T Consensus        71 l~l~~~qV~vWFqNRR~k~kk~~   93 (97)
T 1b72_A           71 LELNETQVKIWFQNRRMKQKKRE   93 (97)
T ss_dssp             HTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hCCCHHHhHHHHHHHhHHHhHHh
Confidence            99999999999999999999865
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Back     alignment and structure
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Back     alignment and structure
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Back     alignment and structure
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Back     alignment and structure
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Back     alignment and structure
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Back     alignment and structure
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Back     alignment and structure
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Back     alignment and structure
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Back     alignment and structure
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Back     alignment and structure
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Back     alignment and structure
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Back     alignment and structure
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Back     alignment and structure
>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Back     alignment and structure
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Back     alignment and structure
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B* Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P Back     alignment and structure
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Back     alignment and structure
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens} Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Back     alignment and structure
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Back     alignment and structure
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Back     alignment and structure
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Back     alignment and structure
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens} Back     alignment and structure
>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A Back     alignment and structure
>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1 Back     alignment and structure
>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D Back     alignment and structure
>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1 Back     alignment and structure
>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1 Back     alignment and structure
>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A Back     alignment and structure
>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 255
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 2e-14
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 2e-14
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 1e-13
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 1e-13
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 2e-13
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 2e-13
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 5e-13
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 2e-12
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 2e-12
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 2e-12
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 4e-12
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 4e-12
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 5e-12
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 1e-11
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 2e-11
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 2e-11
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 2e-11
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 2e-11
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 3e-11
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 3e-11
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 4e-11
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 4e-11
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 6e-11
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 9e-11
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 1e-10
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 3e-10
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 4e-10
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 8e-10
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 3e-09
d2ecca176 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H 7e-09
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 3e-07
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 7e-06
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.1 bits (156), Expect = 2e-14
 Identities = 23/54 (42%), Positives = 31/54 (57%)

Query: 48  KKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEELGLQPRQIAVWFQNRRARLK 101
            + R + DQ   LEK FE    L P  + +LA+ L L  RQ+  WFQNRRA+ +
Sbjct: 3   GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 56
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72 Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53 Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58 Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59 Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58 Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52 Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 Back     information, alignment and structure
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67 Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71 Back     information, alignment and structure
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80 Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Length = 82 Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query255
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.82
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.8
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.79
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.78
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.77
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.77
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.77
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.77
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.76
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.75
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.75
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.75
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.73
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.72
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.72
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.71
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.71
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.7
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.7
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.7
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.69
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.67
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.66
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.65
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.61
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.61
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.61
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.6
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.58
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.56
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.53
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.49
d1hlva166 DNA-binding domain of centromere binding protein B 91.92
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.5e-21  Score=144.71  Aligned_cols=86  Identities=29%  Similarity=0.526  Sum_probs=62.2

Q ss_pred             CCcCCCCcccccccccccccCcchhhhhcccchhhhhhhhccCCCCCCcCCHHHHHHHHHHhHhcCCCCHHHHHHHHHHh
Q 025268            3 SETFDHFHEDKTSTKRKQIYGREFQAMMDCLEEEDCREEASQATEKKRRLTVDQVKALEKNFEVDNKLEPDRKVKLAEEL   82 (255)
Q Consensus         3 ~q~~~w~~e~~~~~~~~~~~~~e~~~m~~~~~~~~~~~~~~~~~~kr~r~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~L   82 (255)
                      ..+|+||+..+..+......+                ...+.++++|++||..|+.+||..|..++||+..++++||..|
T Consensus         1 ~~~y~wm~~~r~~p~~~~~~~----------------~~~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l   64 (88)
T d1b72a_           1 ARTFDWMKVKRNPPKTAKVSE----------------PGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATL   64 (88)
T ss_dssp             CCCCGGGGC------------------------------------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             CCCCCCCcCCCCCCCCCCCCC----------------CCCCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHc
Confidence            368999988873333211111                1112345667789999999999999999999999999999999


Q ss_pred             CCCcchhhhhhhhhHHHhhHHH
Q 025268           83 GLQPRQIAVWFQNRRARLKSKE  104 (255)
Q Consensus        83 gL~~rqVqvWFQNRRak~Kkk~  104 (255)
                      ||++++|+|||||||+|+|+..
T Consensus        65 ~l~~~~V~vWFqNrR~k~Kk~~   86 (88)
T d1b72a_          65 ELNETQVKIWFQNRRMKQKKRE   86 (88)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHeeeccHhHHHHHHHhc
Confidence            9999999999999999999864
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure