Psyllid ID: psy3735

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-
MGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY
cccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHcHHHHHHHcccccccEEEEccccccccccccc
ccccccccccccccccccccccccHHHccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccHHEEEEEEcccccccccccc
mgvpssgrgeedvsegemedyaslpkrkqrryrttFTSFQLEELEKAFsrthypdvftrqcgrfsrqrsmpgelCVAWTHHLNaaftssky
mgvpssgrgeedvsegemedyaslpkrkqrryRTTFTSFQLEELEkafsrthypdvFTRQCGRFSRQRSMPGELCVAWTHHlnaaftssky
MGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY
*********************************TTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAF*****
**********************************TFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLN*AF*****
**********************SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY
******************************RYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHL*********
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MGVPSSGRGEEDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSSKY
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 ?
Query91 2.2.26 [Sep-21-2011]
Q06453 408 Homeobox protein aristale yes N/A 0.593 0.132 0.716 6e-16
A6YP92 566 Homeobox protein ARX OS=R yes N/A 0.384 0.061 0.857 7e-12
Q96QS3 562 Homeobox protein ARX OS=H yes N/A 0.384 0.062 0.857 7e-12
O35085 564 Homeobox protein ARX OS=M yes N/A 0.384 0.062 0.857 8e-12
O42115 453 Aristaless-related homeob yes N/A 0.384 0.077 0.857 1e-11
Q26657327 Aristaless homeobox prote no N/A 0.384 0.107 0.857 2e-11
P47239 503 Paired box protein Pax-7 no N/A 0.483 0.087 0.688 2e-10
P23759 520 Paired box protein Pax-7 no N/A 0.483 0.084 0.688 2e-10
P06601 613 Segmentation protein pair no N/A 0.549 0.081 0.588 4e-10
P09083 449 Protein gooseberry-neuro no N/A 0.549 0.111 0.627 5e-10
>sp|Q06453|AL_DROME Homeobox protein aristaless OS=Drosophila melanogaster GN=al PE=1 SV=2 Back     alignment and function desciption
 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 43/60 (71%), Positives = 48/60 (80%), Gaps = 6/60 (10%)

Query: 5   SSGRGEEDVSEG----EMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
           +SG     VS+G    E ++YA  PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 59  ASGGTNSPVSDGNSDCEADEYA--PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRE 116
Involved in the morphogenesis of proximal and distal pattern elements in a subset of appendages. Also has a role in early imaginal disk development.
Drosophila melanogaster (taxid: 7227)
>sp|A6YP92|ARX_RAT Homeobox protein ARX OS=Rattus norvegicus GN=Arx PE=2 SV=1 Back     alignment and function description
>sp|Q96QS3|ARX_HUMAN Homeobox protein ARX OS=Homo sapiens GN=ARX PE=1 SV=1 Back     alignment and function description
>sp|O35085|ARX_MOUSE Homeobox protein ARX OS=Mus musculus GN=Arx PE=2 SV=3 Back     alignment and function description
>sp|O42115|ARX_DANRE Aristaless-related homeobox protein OS=Danio rerio GN=arx PE=2 SV=1 Back     alignment and function description
>sp|Q26657|ALX_STRPU Aristaless homeobox protein (Fragment) OS=Strongylocentrotus purpuratus GN=ALX PE=2 SV=2 Back     alignment and function description
>sp|P47239|PAX7_MOUSE Paired box protein Pax-7 OS=Mus musculus GN=Pax7 PE=2 SV=2 Back     alignment and function description
>sp|P23759|PAX7_HUMAN Paired box protein Pax-7 OS=Homo sapiens GN=PAX7 PE=2 SV=3 Back     alignment and function description
>sp|P06601|PRD_DROME Segmentation protein paired OS=Drosophila melanogaster GN=prd PE=1 SV=1 Back     alignment and function description
>sp|P09083|GSBN_DROME Protein gooseberry-neuro OS=Drosophila melanogaster GN=gsb-n PE=1 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 ?
Query91
194766533 405 GF20646 [Drosophila ananassae] gi|190617 0.494 0.111 0.851 9e-15
195032675 376 GH11220 [Drosophila grimshawi] gi|193904 0.494 0.119 0.851 1e-14
383865116 261 PREDICTED: homeobox protein aristaless-l 0.494 0.172 0.851 2e-14
424034 384 transcription factor with prd-type homeo 0.593 0.140 0.716 2e-14
350425133 385 PREDICTED: homeobox protein ARX-like [Bo 0.494 0.116 0.851 2e-14
345491839 421 PREDICTED: aristaless-related homeobox p 0.494 0.106 0.829 2e-14
195350083 410 GM16736 [Drosophila sechellia] gi|195575 0.593 0.131 0.716 2e-14
24580629 408 aristaless [Drosophila melanogaster] gi| 0.593 0.132 0.716 2e-14
340709231 280 PREDICTED: homeobox protein aristaless-l 0.494 0.160 0.851 2e-14
290262 408 prd-like homeobox protein [Drosophila me 0.593 0.132 0.716 3e-14
>gi|194766533|ref|XP_001965379.1| GF20646 [Drosophila ananassae] gi|190617989|gb|EDV33513.1| GF20646 [Drosophila ananassae] Back     alignment and taxonomy information
 Score = 84.3 bits (207), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 40/47 (85%), Positives = 44/47 (93%), Gaps = 2/47 (4%)

Query: 14  SEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
           S+GE ++YA  PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 69  SDGEADEYA--PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRE 113

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|195032675|ref|XP_001988540.1| GH11220 [Drosophila grimshawi] gi|193904540|gb|EDW03407.1| GH11220 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|383865116|ref|XP_003708021.1| PREDICTED: homeobox protein aristaless-like [Megachile rotundata] Back     alignment and taxonomy information
>gi|424034|pir||A46403 transcription factor with prd-type homeo domain and Pro/ Gln-rich domain al - fruit fly (Drosophila melanogaster) Back     alignment and taxonomy information
>gi|350425133|ref|XP_003494022.1| PREDICTED: homeobox protein ARX-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|345491839|ref|XP_001607712.2| PREDICTED: aristaless-related homeobox protein-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|195350083|ref|XP_002041571.1| GM16736 [Drosophila sechellia] gi|195575531|ref|XP_002077631.1| GD23020 [Drosophila simulans] gi|194123344|gb|EDW45387.1| GM16736 [Drosophila sechellia] gi|194189640|gb|EDX03216.1| GD23020 [Drosophila simulans] Back     alignment and taxonomy information
>gi|24580629|ref|NP_722629.1| aristaless [Drosophila melanogaster] gi|60416352|sp|Q06453.2|AL_DROME RecName: Full=Homeobox protein aristaless gi|7296213|gb|AAF51505.1| aristaless [Drosophila melanogaster] gi|21464440|gb|AAM52023.1| RE68460p [Drosophila melanogaster] gi|220942482|gb|ACL83784.1| al-PA [synthetic construct] gi|220952686|gb|ACL88886.1| al-PA [synthetic construct] Back     alignment and taxonomy information
>gi|340709231|ref|XP_003393215.1| PREDICTED: homeobox protein aristaless-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|290262|gb|AAA28840.1| prd-like homeobox protein [Drosophila melanogaster] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query91
FB|FBgn0000061 408 al "aristaless" [Drosophila me 0.593 0.132 0.716 1.2e-15
UNIPROTKB|I3LRI8 451 I3LRI8 "Uncharacterized protei 0.560 0.113 0.666 2.2e-12
ZFIN|ZDB-GENE-990415-15 453 arxa "aristaless related homeo 0.560 0.112 0.666 2.2e-12
UNIPROTKB|J9NW39 520 ARX "Uncharacterized protein" 0.560 0.098 0.666 2.9e-12
UNIPROTKB|Q96QS3 562 ARX "Homeobox protein ARX" [Ho 0.560 0.090 0.666 3.4e-12
UNIPROTKB|E2QVR4 564 ARX "Uncharacterized protein" 0.560 0.090 0.666 3.4e-12
MGI|MGI:1097716 564 Arx "aristaless related homeob 0.560 0.090 0.666 3.4e-12
RGD|1562672 566 Arx "aristaless related homeob 0.560 0.090 0.666 3.4e-12
UNIPROTKB|D4A5S8 566 Arx "Homeobox protein ARX" [Ra 0.560 0.090 0.666 3.4e-12
UNIPROTKB|F1LQW2 566 Arx "Homeobox protein ARX" [Ra 0.560 0.090 0.666 3.4e-12
FB|FBgn0000061 al "aristaless" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 202 (76.2 bits), Expect = 1.2e-15, P = 1.2e-15
 Identities = 43/60 (71%), Positives = 48/60 (80%)

Query:     5 SSGRGEEDVSEG----EMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
             +SG     VS+G    E ++YA  PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct:    59 ASGGTNSPVSDGNSDCEADEYA--PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRE 116
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;NAS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0005634 "nucleus" evidence=ISS;NAS
GO:0007449 "proximal/distal pattern formation, imaginal disc" evidence=NAS
GO:0048800 "antennal morphogenesis" evidence=IMP
GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA
GO:0035015 "elongation of arista core" evidence=IMP
GO:0045747 "positive regulation of Notch signaling pathway" evidence=IEP
GO:0035218 "leg disc development" evidence=IMP
GO:0022416 "chaeta development" evidence=IMP
GO:0043234 "protein complex" evidence=IPI
GO:0043565 "sequence-specific DNA binding" evidence=IDA;IPI
GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IMP
GO:0007480 "imaginal disc-derived leg morphogenesis" evidence=IMP
UNIPROTKB|I3LRI8 I3LRI8 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-990415-15 arxa "aristaless related homeobox a" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|J9NW39 ARX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q96QS3 ARX "Homeobox protein ARX" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E2QVR4 ARX "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
MGI|MGI:1097716 Arx "aristaless related homeobox" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1562672 Arx "aristaless related homeobox" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|D4A5S8 Arx "Homeobox protein ARX" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|F1LQW2 Arx "Homeobox protein ARX" [Rattus norvegicus (taxid:10116)] 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q06453AL_DROMENo assigned EC number0.71660.59340.1323yesN/A

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query91
pfam0004657 pfam00046, Homeobox, Homeobox domain 1e-09
smart0038957 smart00389, HOX, Homeodomain 1e-07
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 2e-07
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 49.0 bits (118), Expect = 1e-09
 Identities = 18/31 (58%), Positives = 20/31 (64%)

Query: 30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          RR RTTFT  QLEELEK F +  YP    R+
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEERE 31

Length = 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>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

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 91
KOG0484|consensus125 99.91
KOG0488|consensus309 99.89
KOG0850|consensus245 99.88
KOG0489|consensus261 99.87
KOG0485|consensus 268 99.85
KOG0842|consensus307 99.85
KOG0494|consensus 332 99.85
KOG0843|consensus197 99.84
KOG0487|consensus308 99.83
KOG2251|consensus 228 99.81
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.8
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.79
KOG0492|consensus246 99.79
KOG0493|consensus342 99.73
KOG0848|consensus317 99.72
KOG3802|consensus398 99.72
COG5576156 Homeodomain-containing transcription factor [Trans 99.71
KOG0483|consensus198 99.71
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.69
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.69
KOG0486|consensus 351 99.68
KOG0844|consensus 408 99.68
KOG0491|consensus194 99.64
KOG4577|consensus 383 99.63
KOG0847|consensus288 99.62
KOG0490|consensus 235 99.61
KOG0849|consensus 354 99.49
KOG1168|consensus385 99.49
KOG0775|consensus304 98.79
KOG2252|consensus558 98.78
KOG0490|consensus235 98.74
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.59
KOG0774|consensus334 98.56
KOG1146|consensus 1406 98.26
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 97.17
KOG3623|consensus 1007 96.75
KOG0773|consensus342 96.57
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 95.58
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 91.1
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 82.33
COG3413215 Predicted DNA binding protein [General function pr 80.97
>KOG0484|consensus Back     alignment and domain information 
Probab=99.91  E-value=1e-25  Score=126.66  Aligned_cols=63  Identities=44%  Similarity=0.679  Sum_probs=59.6

Q ss_pred             ccCCCCCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735          25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS   89 (91)
Q Consensus        25 ~~~k~~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~   89 (91)
                      ..++.+|.||.||..||.+||..|...|||++.+|++|  |..+.|++..|||||||||+|++++
T Consensus        13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEi--A~kidLTEARVQVWFQNRRAKfRKQ   75 (125)
T KOG0484|consen   13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEI--ALKIDLTEARVQVWFQNRRAKFRKQ   75 (125)
T ss_pred             HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHH--HHhhhhhHHHHHHHHHhhHHHHHHH
Confidence            46678889999999999999999999999999999999  9999999999999999999999875

>KOG0488|consensus Back     alignment and domain information
>KOG0850|consensus Back     alignment and domain information
>KOG0489|consensus Back     alignment and domain information
>KOG0485|consensus Back     alignment and domain information
>KOG0842|consensus Back     alignment and domain information
>KOG0494|consensus Back     alignment and domain information
>KOG0843|consensus Back     alignment and domain information
>KOG0487|consensus Back     alignment and domain information
>KOG2251|consensus Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0492|consensus Back     alignment and domain information
>KOG0493|consensus Back     alignment and domain information
>KOG0848|consensus Back     alignment and domain information
>KOG3802|consensus Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0483|consensus Back     alignment and domain information
>smart00389 HOX Homeodomain 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
>KOG0486|consensus Back     alignment and domain information
>KOG0844|consensus Back     alignment and domain information
>KOG0491|consensus Back     alignment and domain information
>KOG4577|consensus Back     alignment and domain information
>KOG0847|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>KOG1168|consensus Back     alignment and domain information
>KOG0775|consensus Back     alignment and domain information
>KOG2252|consensus Back     alignment and domain information
>KOG0490|consensus 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
>KOG0774|consensus Back     alignment and domain information
>KOG1146|consensus Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>KOG3623|consensus Back     alignment and domain information
>KOG0773|consensus 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
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>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
>COG3413 Predicted DNA binding protein [General function prediction only] 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 ?
Query91
3a01_B67 Crystal Structure Of Aristaless And Clawless Homeod 7e-15
3lnq_A58 Structure Of Aristaless Homeodomain In Complex With 3e-11
1fjl_A81 Homeodomain From The Drosophila Paired Protein Boun 3e-10
3a02_A60 Crystal Structure Of Aristaless Homeodomain Length 6e-09
2m0c_A75 Solution Nmr Structure Of Homeobox Domain Of Human 8e-09
3cmy_A61 Structure Of A Homeodomain In Complex With Dna Leng 1e-08
2cue_A80 Solution Structure Of The Homeobox Domain Of The Hu 2e-06
2l7m_P68 Solution Structure Of The Pitx2 Homeodomain R24h Mu 2e-05
2dms_A80 Solution Structure Of The Homeobox Domain Of Homeob 9e-05
2l7f_P68 Solution Structure Of The Pitx2 Homeodomain Length 2e-04
2dmu_A70 Solution Structure Of The Homeobox Domain Of Homeob 2e-04
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67 Back     alignment and structure 
Iteration: 1

 Score = 75.5 bits (184), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 35/36 (97%), Positives = 36/36 (100%)
Query: 25 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
          PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR+
Sbjct: 2  PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRE 37
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58 Back     alignment and structure
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81 Back     alignment and structure
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60 Back     alignment and structure
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4, Northeast Structural Genomics Consortium (Nesg) Target Hr4490c Length = 75 Back     alignment and structure
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna Length = 61 Back     alignment and structure
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human Paired Box Protein Pax-6 Length = 80 Back     alignment and structure
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant Length = 68 Back     alignment and structure
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Otx2 Length = 80 Back     alignment and structure
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain Length = 68 Back     alignment and structure
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70 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 ?
Query91
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 8e-21
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 5e-19
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 1e-18
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 5e-18
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 1e-17
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 1e-16
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 1e-15
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 1e-15
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 9e-15
3a02_A60 Homeobox protein aristaless; homeodomain, developm 1e-14
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 8e-14
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 2e-13
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 1e-11
1uhs_A72 HOP, homeodomain only protein; structural genomics 9e-11
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 1e-10
1lfb_A99 Liver transcription factor (LFB1); transcription r 1e-10
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 1e-09
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 2e-09
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 1e-08
3d1n_I151 POU domain, class 6, transcription factor 1; prote 4e-08
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 1e-07
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 4e-07
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 7e-07
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 8e-06
2xsd_C164 POU domain, class 3, transcription factor 1; trans 9e-06
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 3e-05
1e3o_C160 Octamer-binding transcription factor 1; transcript 3e-05
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 4e-05
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 4e-05
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 5e-05
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 6e-05
3a01_A93 Homeodomain-containing protein; homeodomain, prote 6e-05
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 6e-05
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 1e-04
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 1e-04
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 1e-04
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 2e-04
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 2e-04
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 3e-04
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 3e-04
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 3e-04
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 4e-04
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 8e-04
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 9e-04
>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
 Score = 77.4 bits (191), Expect = 8e-21
 Identities = 30/49 (61%), Positives = 39/49 (79%), Gaps = 1/49 (2%)

Query: 11 EDVSEGEMEDYASLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTR 59
          ED+S+ E E   +L KRKQRR RTTF++ QL+ELE+AF RT YPD++TR
Sbjct: 1  EDISDCESEPGIAL-KRKQRRSRTTFSASQLDELERAFERTQYPDIYTR 48
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95 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
>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
>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
>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 Length = 194 Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221 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
>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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query91
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.92
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.92
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.92
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.92
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.92
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.91
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.91
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.91
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.91
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.91
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.91
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.9
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.9
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.9
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.9
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.9
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.9
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.9
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.9
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.9
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.9
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.89
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.89
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.89
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.89
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.89
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.89
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.89
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.89
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.89
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.89
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.89
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.89
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.88
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.88
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.88
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.88
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.88
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.88
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.88
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.88
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.88
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.88
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.87
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.87
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.87
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.87
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.87
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.87
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.86
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.86
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.86
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.86
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.85
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.85
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.85
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.85
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.85
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.84
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.84
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.84
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.84
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.84
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.83
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.83
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.83
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.83
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.83
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.83
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.81
2e19_A64 Transcription factor 8; homeobox domain, structura 99.81
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.74
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.73
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.7
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.67
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.58
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.55
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 99.27
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 95.94
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 85.92
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 85.48
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 81.87
>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
Probab=99.92  E-value=5.8e-26  Score=123.96  Aligned_cols=62  Identities=24%  Similarity=0.223  Sum_probs=58.1

Q ss_pred             cCCCCCCCCCCCHHHHHHHHHHHhh----CCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhcC
Q psy3735          26 KRKQRRYRTTFTSFQLEELEKAFSR----THYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTSS   89 (91)
Q Consensus        26 ~~k~~r~R~~~t~~ql~~Le~~f~~----~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~~   89 (91)
                      ..+.++.||.||.+|+..|+..|+.    ++||+..+++.|  |..|||++.+|+|||||||+|++++
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~L--a~~lgL~~~~VkvWFqNrRaK~~~~   79 (80)
T 1wh5_A           14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRF--CQETGVPRQVLKVWLHNNKHSGPSS   79 (80)
T ss_dssp             CCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHH--HHHSCCCHHHHHHHHHHHSSSSSCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHH--HHHhCCCcccccCCccccCcCCCCC
Confidence            3457788999999999999999999    999999999999  9999999999999999999999875
>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
>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
>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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} 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
>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
>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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* 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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>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
>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
>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
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} 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
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {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
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>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
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A 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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A 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
>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
>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
>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
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} 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
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {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
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} 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 91
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 6e-10
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 1e-08
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 3e-08
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 6e-08
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 8e-08
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 9e-08
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 1e-07
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 1e-07
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 1e-07
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 2e-07
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 2e-07
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 4e-07
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 5e-07
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 7e-07
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 9e-07
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 2e-06
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 4e-06
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 5e-06
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 8e-06
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 3e-05
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 5e-05
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 7e-05
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 0.003
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 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-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.7 bits (116), Expect = 6e-10
 Identities = 13/38 (34%), Positives = 15/38 (39%)

Query: 23 SLPKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTRQ 60
           L  R  R+ R  +T  Q  ELEK F    Y     R 
Sbjct: 7  WLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRY 44
>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
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 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
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 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
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 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
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 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
>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
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 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
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58 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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query91
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.93
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.93
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.93
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.92
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.92
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.92
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.92
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.92
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.92
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.91
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.91
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.9
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.9
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.9
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.9
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.9
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.9
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.9
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.89
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.89
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.89
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.88
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.87
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.86
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.83
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.82
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.81
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.8
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.79
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.76
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.76
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.72
d1hlva166 DNA-binding domain of centromere binding protein B 91.52
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 88.35
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {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-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.93  E-value=3.1e-27  Score=120.33  Aligned_cols=57  Identities=19%  Similarity=0.266  Sum_probs=54.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHhhCCCCCHHHhhhhhhhhhcCCCCCcchhccchhHHhhhc
Q psy3735          30 RRYRTTFTSFQLEELEKAFSRTHYPDVFTRQCGRFSRQRSMPGELCVAWTHHLNAAFTS   88 (91)
Q Consensus        30 ~r~R~~~t~~ql~~Le~~f~~~~~p~~~~r~~l~~a~~l~l~~~~v~vWFqnrR~k~~~   88 (91)
                      ++.|+.||.+|+..|+..|..++||+...+..|  |..|||++.+|+|||||||+|+++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~L--A~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKI--SAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHH--HHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHH--HHHcCCCHHHeeecccchhhhccC
Confidence            567899999999999999999999999999999  999999999999999999999875
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} 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
>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
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} 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
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>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
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure