Psyllid ID: psy9614

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---
MFFYFFPPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSDFTSKCAETLAHKQTKRES
cccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHccccccEEEEEEccccccccccccHHHccccccccccccHHHHccccccc
ccccccccccccccHccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccc
mffyffppgsankprkirrsrttfTTYQLHQLERafdktqypdvftreDLASRLDLSEarvqvnsdsqiptlgsneKVQIVVTSDFTSKCAETLAhkqtkres
mffyffppgsankprkirrsRTTFTTYQLHqlerafdktqypdVFTREDLASrldlsearvqvnsdsqiptlgsnekVQIVVTSDFTSKCAetlahkqtkres
MFFYFFPPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSDFTSKCAETLAHKQTKRES
**FYFF***************TTFTTYQLHQLERAFDKTQYPDVFTRED****************************VQIVVTSDFT****************
**********************TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDS************************************
MFFYFFPPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSDFTSKC*************
******************RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEK**************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MFFYFFPPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVTSDFTSKCAETLAHKQTKRES
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 ?
Query103 2.2.26 [Sep-21-2011]
Q96QS3 562 Homeobox protein ARX OS=H yes N/A 0.475 0.087 0.795 6e-16
A6YP92 566 Homeobox protein ARX OS=R yes N/A 0.475 0.086 0.795 6e-16
O35085 564 Homeobox protein ARX OS=M yes N/A 0.475 0.086 0.795 7e-16
O42115 453 Aristaless-related homeob no N/A 0.475 0.108 0.795 1e-15
Q26657327 Aristaless homeobox prote no N/A 0.475 0.149 0.775 8e-15
Q9I9A2 327 Retinal homeobox protein N/A N/A 0.475 0.149 0.673 9e-15
Q9PVY0 228 Retinal homeobox protein yes N/A 0.553 0.25 0.6 2e-14
O42567 325 Retinal homeobox protein N/A N/A 0.475 0.150 0.673 2e-14
Q9I9D5 334 Retinal homeobox protein N/A N/A 0.533 0.164 0.625 2e-14
O97039268 Retinal homeobox protein N/A N/A 0.553 0.212 0.614 2e-14
>sp|Q96QS3|ARX_HUMAN Homeobox protein ARX OS=Homo sapiens GN=ARX PE=1 SV=1 Back     alignment and function desciption
 Score = 82.8 bits (203), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 39/49 (79%), Positives = 43/49 (87%)

Query: 15  RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
           RK RR RTTFT+YQL +LERAF KT YPDVFTRE+LA RLDL+EARVQV
Sbjct: 326 RKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQV 374
Transcription factor required for normal brain development. May be important for maintenance of specific neuronal subtypes in the cerebral cortex and axonal guidance in the floor plate.
Homo sapiens (taxid: 9606)
>sp|A6YP92|ARX_RAT Homeobox protein ARX OS=Rattus norvegicus GN=Arx PE=2 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|Q9I9A2|RX2_ORYLA Retinal homeobox protein Rx2 OS=Oryzias latipes GN=rx2 PE=2 SV=1 Back     alignment and function description
>sp|Q9PVY0|RX1_CHICK Retinal homeobox protein Rx1 OS=Gallus gallus GN=RX1 PE=2 SV=1 Back     alignment and function description
>sp|O42567|RXB_XENLA Retinal homeobox protein Rx-B OS=Xenopus laevis GN=rax-b PE=2 SV=2 Back     alignment and function description
>sp|Q9I9D5|RX1_ASTFA Retinal homeobox protein Rx1 OS=Astyanax fasciatus GN=rx1 PE=2 SV=1 Back     alignment and function description
>sp|O97039|RX_DUGJA Retinal homeobox protein Rax (Fragment) OS=Dugesia japonica GN=RAX PE=2 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query103
157122925 289 paired box protein, putative [Aedes aegy 0.543 0.193 0.857 2e-20
295389208 294 homeobrain [Nematostella vectensis] 0.533 0.187 0.872 3e-20
156386935 214 predicted protein [Nematostella vectensi 0.533 0.257 0.872 3e-20
312372108 241 hypothetical protein AND_20593 [Anophele 0.553 0.236 0.824 3e-20
195029473 395 GH19875 [Drosophila grimshawi] gi|193903 0.533 0.139 0.854 4e-20
195401625 405 GJ18584 [Drosophila virilis] gi|19414241 0.533 0.135 0.854 4e-20
405961985 442 Homeobox protein ARX [Crassostrea gigas] 0.514 0.119 0.905 4e-20
195119468 411 GI19825 [Drosophila mojavensis] gi|19390 0.533 0.133 0.854 4e-20
291222403 379 PREDICTED: predicted protein-like [Sacco 0.495 0.134 0.921 5e-20
270010993 261 homeobrain [Tribolium castaneum] 0.495 0.195 0.921 7e-20
>gi|157122925|ref|XP_001659959.1| paired box protein, putative [Aedes aegypti] gi|108882959|gb|EAT47184.1| AAEL001696-PA [Aedes aegypti] Back     alignment and taxonomy information
 Score =  102 bits (255), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/56 (85%), Positives = 52/56 (92%)

Query: 8   PGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
           P   N+PRKIRRSRTTFTT+QLHQLERAF+KTQYPDVFTRE+LA RLDLSEARVQV
Sbjct: 87  PNDMNRPRKIRRSRTTFTTFQLHQLERAFEKTQYPDVFTREELAMRLDLSEARVQV 142

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|295389208|gb|ADG03434.1| homeobrain [Nematostella vectensis] Back     alignment and taxonomy information
>gi|156386935|ref|XP_001634166.1| predicted protein [Nematostella vectensis] gi|156221246|gb|EDO42103.1| predicted protein [Nematostella vectensis] Back     alignment and taxonomy information
>gi|312372108|gb|EFR20142.1| hypothetical protein AND_20593 [Anopheles darlingi] Back     alignment and taxonomy information
>gi|195029473|ref|XP_001987597.1| GH19875 [Drosophila grimshawi] gi|193903597|gb|EDW02464.1| GH19875 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|195401625|ref|XP_002059413.1| GJ18584 [Drosophila virilis] gi|194142419|gb|EDW58825.1| GJ18584 [Drosophila virilis] Back     alignment and taxonomy information
>gi|405961985|gb|EKC27709.1| Homeobox protein ARX [Crassostrea gigas] Back     alignment and taxonomy information
>gi|195119468|ref|XP_002004253.1| GI19825 [Drosophila mojavensis] gi|193909321|gb|EDW08188.1| GI19825 [Drosophila mojavensis] Back     alignment and taxonomy information
>gi|291222403|ref|XP_002731203.1| PREDICTED: predicted protein-like [Saccoglossus kowalevskii] Back     alignment and taxonomy information
>gi|270010993|gb|EFA07441.1| homeobrain [Tribolium castaneum] 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 ?
Query103
FB|FBgn0008636 409 hbn "homeobrain" [Drosophila m 0.495 0.124 0.901 5.3e-20
UNIPROTKB|F1NH36 262 Gga.55791 "Uncharacterized pro 0.553 0.217 0.616 8.8e-15
UNIPROTKB|Q9PVY0 228 RX1 "Retinal homeobox protein 0.553 0.25 0.616 8.8e-15
UNIPROTKB|E2R5X4184 RAX2 "Uncharacterized protein" 0.543 0.304 0.625 8.8e-15
UNIPROTKB|I3LRI8 451 I3LRI8 "Uncharacterized protei 0.475 0.108 0.795 8.9e-15
ZFIN|ZDB-GENE-990415-15 453 arxa "aristaless related homeo 0.475 0.108 0.795 9e-15
UNIPROTKB|J9NW39 520 ARX "Uncharacterized protein" 0.475 0.094 0.795 1.2e-14
UNIPROTKB|Q96QS3 562 ARX "Homeobox protein ARX" [Ho 0.475 0.087 0.795 1.4e-14
UNIPROTKB|E2QVR4 564 ARX "Uncharacterized protein" 0.475 0.086 0.795 1.4e-14
MGI|MGI:1097716 564 Arx "aristaless related homeob 0.475 0.086 0.795 1.4e-14
FB|FBgn0008636 hbn "homeobrain" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
 Score = 241 (89.9 bits), Expect = 5.3e-20, P = 5.3e-20
 Identities = 46/51 (90%), Positives = 50/51 (98%)

Query:    13 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
             +PRK+RRSRTTFTT+QLHQLERAF+KTQYPDVFTREDLA RLDLSEARVQV
Sbjct:   149 RPRKVRRSRTTFTTFQLHQLERAFEKTQYPDVFTREDLAMRLDLSEARVQV 199
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;NAS
GO:0005634 "nucleus" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0043565 "sequence-specific DNA binding" evidence=IEA
UNIPROTKB|F1NH36 Gga.55791 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q9PVY0 RX1 "Retinal homeobox protein Rx1" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2R5X4 RAX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
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

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) ?
A6YP92ARX_RATNo assigned EC number0.79590.47570.0865yesN/A
Q96QS3ARX_HUMANNo assigned EC number0.79590.47570.0871yesN/A
Q94398HM08_CAEELNo assigned EC number0.67340.47570.1775yesN/A
O35085ARX_MOUSENo assigned EC number0.79590.47570.0868yesN/A
Q9PVY0RX1_CHICKNo assigned EC number0.60.55330.25yesN/A
A2T711RAX2_PANTRNo assigned EC number0.67340.47570.2663yesN/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 ?
Query103
pfam0004657 pfam00046, Homeobox, Homeobox domain 1e-16
smart0038957 smart00389, HOX, Homeodomain 2e-13
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 3e-13
COG5576156 COG5576, COG5576, Homeodomain-containing transcrip 3e-04
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 67.5 bits (166), Expect = 1e-16
 Identities = 24/46 (52%), Positives = 33/46 (71%)

Query: 18 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
          RR RTTFT  QL +LE+ F+K +YP    RE+LA +L L+E +V+V
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKV 46

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
>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 103
KOG0484|consensus125 99.87
KOG0850|consensus245 99.85
KOG0488|consensus309 99.84
KOG2251|consensus 228 99.83
KOG0489|consensus261 99.82
KOG0842|consensus307 99.82
KOG0843|consensus197 99.81
KOG0494|consensus 332 99.79
KOG0487|consensus308 99.78
KOG0485|consensus268 99.76
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.75
KOG0492|consensus246 99.74
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.73
KOG0848|consensus317 99.7
KOG0493|consensus342 99.7
KOG0844|consensus 408 99.69
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.66
KOG0486|consensus 351 99.65
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.64
KOG3802|consensus398 99.64
COG5576156 Homeodomain-containing transcription factor [Trans 99.63
KOG0491|consensus194 99.61
KOG4577|consensus 383 99.58
KOG0483|consensus198 99.58
KOG0847|consensus288 99.51
KOG0490|consensus235 99.5
KOG0849|consensus354 99.36
KOG1168|consensus385 99.19
KOG0775|consensus304 99.1
KOG0774|consensus334 98.74
KOG2252|consensus558 98.62
KOG0490|consensus235 98.53
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.5
KOG1146|consensus 1406 98.01
KOG0773|consensus342 97.26
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 97.1
KOG3623|consensus 1007 96.86
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 95.09
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 91.02
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 82.9
KOG1146|consensus 1406 82.63
>KOG0484|consensus Back     alignment and domain information 
Probab=99.87  E-value=8.4e-24  Score=130.48  Aligned_cols=70  Identities=46%  Similarity=0.710  Sum_probs=65.0

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccc
Q psy9614          10 SANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQ   79 (103)
Q Consensus        10 ~~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~   79 (103)
                      +-...++++|-||.|+..||..||+.|...+||++-+|++||..++|++.+|||||||||+|+||+++..
T Consensus        10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            3345688999999999999999999999999999999999999999999999999999999999988763

>KOG0850|consensus Back     alignment and domain information
>KOG0488|consensus Back     alignment and domain information
>KOG2251|consensus Back     alignment and domain information
>KOG0489|consensus Back     alignment and domain information
>KOG0842|consensus Back     alignment and domain information
>KOG0843|consensus Back     alignment and domain information
>KOG0494|consensus Back     alignment and domain information
>KOG0487|consensus Back     alignment and domain information
>KOG0485|consensus Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0492|consensus Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0848|consensus Back     alignment and domain information
>KOG0493|consensus Back     alignment and domain information
>KOG0844|consensus Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG0486|consensus 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
>KOG3802|consensus Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0491|consensus Back     alignment and domain information
>KOG4577|consensus Back     alignment and domain information
>KOG0483|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
>KOG0774|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
>KOG1146|consensus Back     alignment and domain information
>KOG0773|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
>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
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>KOG1146|consensus 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 ?
Query103
1fjl_A81 Homeodomain From The Drosophila Paired Protein Boun 8e-15
3a01_B67 Crystal Structure Of Aristaless And Clawless Homeod 4e-14
2m0c_A75 Solution Nmr Structure Of Homeobox Domain Of Human 8e-14
3cmy_A61 Structure Of A Homeodomain In Complex With Dna Leng 3e-13
3lnq_A58 Structure Of Aristaless Homeodomain In Complex With 2e-12
3a02_A60 Crystal Structure Of Aristaless Homeodomain Length 8e-12
2cue_A80 Solution Structure Of The Homeobox Domain Of The Hu 2e-10
2dms_A80 Solution Structure Of The Homeobox Domain Of Homeob 1e-09
2l7f_P68 Solution Structure Of The Pitx2 Homeodomain Length 2e-07
2l7m_P68 Solution Structure Of The Pitx2 Homeodomain R24h Mu 2e-07
2dmu_A70 Solution Structure Of The Homeobox Domain Of Homeob 2e-07
2dmt_A80 Solution Structure Of The Homeobox Domain Of Homeob 2e-05
2djn_A70 The Solution Structure Of The Homeobox Domain Of Hu 1e-04
2k40_A67 Nmr Structure Of Hesx-1 Homeodomain Double Mutant R 3e-04
1ig7_A58 Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 6e-04
2m34_A71 Nmr Structure Of The Homeodomain Transcription Fact 9e-04
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A Dna Oligonucleotide Length = 81 Back     alignment and structure 
Iteration: 1

 Score = 75.5 bits (184), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 37/56 (66%), Positives = 47/56 (83%), Gaps = 1/56 (1%)
Query: 8  PGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
          PG A K RK RRSRTTF+  QL +LERAF++TQYPD++TRE+LA R +L+EAR+QV
Sbjct: 10 PGIALK-RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 67 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|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna Length = 58 Back     alignment and structure
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain Length = 60 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|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|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant 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
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80 Back     alignment and structure
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5 Length = 70 Back     alignment and structure
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L Length = 67 Back     alignment and structure
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 Back     alignment and structure
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1 From Homo Sapiens Length = 71 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 ?
Query103
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 2e-27
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 6e-27
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 2e-26
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 1e-25
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 4e-25
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 6e-25
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 2e-24
3a02_A60 Homeobox protein aristaless; homeodomain, developm 3e-24
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-23
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 2e-21
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 1e-20
1uhs_A72 HOP, homeodomain only protein; structural genomics 4e-19
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 7e-18
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 1e-17
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 1e-15
3d1n_I151 POU domain, class 6, transcription factor 1; prote 7e-15
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 7e-14
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 8e-14
1lfb_A99 Liver transcription factor (LFB1); transcription r 2e-13
2xsd_C164 POU domain, class 3, transcription factor 1; trans 2e-13
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 1e-12
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 2e-12
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 2e-12
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 2e-11
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 6e-11
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 9e-11
3a01_A93 Homeodomain-containing protein; homeodomain, prote 1e-10
1e3o_C160 Octamer-binding transcription factor 1; transcript 2e-10
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 3e-10
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 3e-10
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 5e-10
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 7e-10
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 1e-09
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 3e-09
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 3e-09
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 6e-09
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 6e-09
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 3e-08
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 1e-07
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 3e-07
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 6e-07
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 8e-07
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 1e-06
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 1e-06
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 2e-06
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 4e-06
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 1e-05
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 1e-05
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 7e-05
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 8e-05
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 9e-05
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 2e-04
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 4e-04
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 5e-04
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 6e-04
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 8e-04
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, 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 = 94.4 bits (235), Expect = 2e-27
 Identities = 33/54 (61%), Positives = 43/54 (79%)

Query: 10 SANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
               RK RRSRTTF+  QL +LERAF++TQYPD++TRE+LA R +L+EAR+QV
Sbjct: 11 GIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQV 64
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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} Length = 102 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
>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
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query103
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.89
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.89
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.89
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.89
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.89
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.89
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.88
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.88
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.88
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.88
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.88
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.88
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.88
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.87
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.87
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.87
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.87
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.87
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.87
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.87
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.87
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.86
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.86
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.86
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.86
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.86
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.86
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.86
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.86
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.86
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.86
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.85
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.85
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.85
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.85
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.85
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.85
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.85
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.84
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.84
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.84
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.84
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.84
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.84
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.84
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.84
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.83
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.83
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.83
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.83
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.82
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.81
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.81
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.81
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.81
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.81
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.81
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.8
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.8
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.8
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.79
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.79
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.79
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.79
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.78
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.78
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.77
2e19_A64 Transcription factor 8; homeobox domain, structura 99.77
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.77
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.76
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.76
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.68
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.65
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.61
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.57
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.5
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.47
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.94
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 96.3
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 86.14
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 82.98
>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
Probab=99.89  E-value=4.3e-24  Score=126.95  Aligned_cols=72  Identities=39%  Similarity=0.505  Sum_probs=65.2

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceecccccccccccccccccccC
Q psy9614          12 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQIVVT   83 (103)
Q Consensus        12 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~~~~   83 (103)
                      +...+.++.|+.|+..|+.+|+..|..++||+..++..||..++|++.+|+|||||||+++|+.+.......
T Consensus         2 s~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~~~~~   73 (80)
T 2dms_A            2 SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGG   73 (80)
T ss_dssp             CCCCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHccCCCC
Confidence            344677899999999999999999999999999999999999999999999999999999999887654433
>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
>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
>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
>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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} 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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* 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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_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
>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
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} 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
>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
>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
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 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
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} 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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} 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
>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
>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
>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 103
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 4e-15
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 6e-14
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 8e-13
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 1e-12
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 1e-12
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 4e-12
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 4e-12
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 7e-12
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 1e-11
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 2e-11
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 2e-11
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 4e-11
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 4e-11
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 4e-11
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 4e-11
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 9e-11
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 2e-10
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 9e-10
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 9e-10
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 2e-09
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 2e-09
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 8e-09
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 8e-09
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 2e-08
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 2e-08
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 4e-08
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 2e-07
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 2e-07
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 4e-07
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 4e-07
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 3e-05
d2ecca176 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H 6e-04
>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 = 62.2 bits (151), Expect = 4e-15
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 7  PPGSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQV 63
          P  +    R  R+ R  +T +Q  +LE+ F    Y     R ++A  L+L+E +V++
Sbjct: 3  PAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI 59
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 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
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 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
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 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
>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
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58 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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 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
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 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
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72 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
>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
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 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
>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
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57 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
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71 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
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query103
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.92
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.91
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.9
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.89
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.89
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.89
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.89
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.89
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.88
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.88
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.88
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.87
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.87
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.87
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.87
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.87
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.86
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.85
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.85
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.84
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.84
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.84
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.83
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.82
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.81
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.78
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.76
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.75
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.74
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.7
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.68
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.66
d1hlva166 DNA-binding domain of centromere binding protein B 91.31
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 86.93
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.92  E-value=7.2e-26  Score=132.46  Aligned_cols=72  Identities=28%  Similarity=0.329  Sum_probs=66.2

Q ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHhcCCCcccceeccccccccccccccccc
Q psy9614           9 GSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQVNSDSQIPTLGSNEKVQI   80 (103)
Q Consensus         9 ~~~~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V~vWFqNrR~k~rr~~~~~~   80 (103)
                      ++++.+.+.++.||+||.+|+.+|+.+|..++||+..++..||..+||++.+|+|||||+|+++|+......
T Consensus         1 ~s~g~p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~   72 (77)
T d1vnda_           1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKG   72 (77)
T ss_dssp             CCSCCSSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCCSS
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhccC
Confidence            356778888999999999999999999999999999999999999999999999999999999998765443
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} 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
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} 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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {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
>d1fjla_ a.4.1.1 (A:) Paired 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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {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
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {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
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} 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
>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