Psyllid ID: psy4349

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
MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccccc
ccccccHHHHHHccccccccccccccccccccccccEEEccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccEEcc
mlhsgdlsssmeslsyesgagnsspgsgvhshqrtkRMRTSFKHHQLRTMKSYFninqnpdakdLKQLAQktglskrvlq
mlhsgdlsSSMESLSYEsgagnsspgsgvhshqRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKqlaqktglskrvlq
MLHsgdlsssmeslsyesgAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ
********************************************************************************
******************************************KHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL*
****************************************SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ
****GDLSSSMES*********************TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKR***
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ
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 ?
Query80 2.2.26 [Sep-21-2011]
Q9Z0S2406 LIM/homeobox protein Lhx2 yes N/A 0.625 0.123 0.9 5e-20
P50458406 LIM/homeobox protein Lhx2 yes N/A 0.625 0.123 0.9 5e-20
P29673469 Protein apterous OS=Droso yes N/A 0.687 0.117 0.836 6e-20
A0JNI8397 LIM/homeobox protein Lhx9 no N/A 0.6 0.120 0.916 7e-20
P36198 426 LIM/homeobox protein Lhx2 no N/A 0.625 0.117 0.9 7e-20
Q1LWV4396 LIM/homeobox protein Lhx9 no N/A 0.6 0.121 0.916 8e-20
Q9NQ69397 LIM/homeobox protein Lhx9 no N/A 0.6 0.120 0.916 8e-20
Q9WUH2397 LIM/homeobox protein Lhx9 no N/A 0.6 0.120 0.916 9e-20
Q68EY3331 LIM/homeobox protein Lhx9 N/A N/A 0.6 0.145 0.916 9e-20
Q80W90388 LIM/homeobox protein Lhx9 no N/A 0.6 0.123 0.916 1e-19
>sp|Q9Z0S2|LHX2_MOUSE LIM/homeobox protein Lhx2 OS=Mus musculus GN=Lhx2 PE=1 SV=1 Back     alignment and function desciption
 Score = 96.3 bits (238), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 45/50 (90%), Positives = 47/50 (94%)

Query: 31  SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80
           S Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 262 SSQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 311
Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.
Mus musculus (taxid: 10090)
>sp|P50458|LHX2_HUMAN LIM/homeobox protein Lhx2 OS=Homo sapiens GN=LHX2 PE=2 SV=2 Back     alignment and function description
>sp|P29673|APTE_DROME Protein apterous OS=Drosophila melanogaster GN=ap PE=2 SV=1 Back     alignment and function description
>sp|A0JNI8|LHX9_BOVIN LIM/homeobox protein Lhx9 OS=Bos taurus GN=LHX9 PE=2 SV=2 Back     alignment and function description
>sp|P36198|LHX2_RAT LIM/homeobox protein Lhx2 OS=Rattus norvegicus GN=Lhx2 PE=2 SV=1 Back     alignment and function description
>sp|Q1LWV4|LHX9_DANRE LIM/homeobox protein Lhx9 OS=Danio rerio GN=lhx9 PE=2 SV=1 Back     alignment and function description
>sp|Q9NQ69|LHX9_HUMAN LIM/homeobox protein Lhx9 OS=Homo sapiens GN=LHX9 PE=1 SV=3 Back     alignment and function description
>sp|Q9WUH2|LHX9_MOUSE LIM/homeobox protein Lhx9 OS=Mus musculus GN=Lhx9 PE=1 SV=3 Back     alignment and function description
>sp|Q68EY3|LHX9_XENLA LIM/homeobox protein Lhx9 OS=Xenopus laevis GN=lhx9 PE=2 SV=1 Back     alignment and function description
>sp|Q80W90|LHX9_RAT LIM/homeobox protein Lhx9 OS=Rattus norvegicus GN=Lhx9 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 ?
Query80
380690603 231 apterous, partial [Cydia pomonella] 0.95 0.329 0.825 4e-28
328925124 349 apterous B alpha [Bombyx mori] 0.962 0.220 0.839 9e-28
328925126159 apterous B beta [Bombyx mori] 0.962 0.484 0.839 9e-28
345487079 406 PREDICTED: LIM/homeobox protein Lhx9-lik 0.975 0.192 0.790 3e-27
357622661 359 apterous [Danaus plexippus] 0.962 0.214 0.827 4e-27
225543484 361 apterous [Tribolium castaneum] gi|224459 0.987 0.218 0.787 1e-26
270004906150 apterous 2 [Tribolium castaneum] 0.987 0.526 0.787 2e-26
340721020 391 PREDICTED: LIM/homeobox protein Lhx9-lik 0.962 0.196 0.765 3e-26
350404759 441 PREDICTED: LIM/homeobox protein Lhx9-lik 0.962 0.174 0.765 3e-26
328787166 390 PREDICTED: LIM/homeobox protein Lhx9-lik 0.962 0.197 0.765 3e-26
>gi|380690603|gb|AFD93370.1| apterous, partial [Cydia pomonella] Back     alignment and taxonomy information
 Score =  128 bits (322), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 66/80 (82%), Positives = 71/80 (88%), Gaps = 4/80 (5%)

Query: 1   MLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNP 60
           +LH GDLSSSMESL+Y+SGA  +SPGS   S  RTKRMRTSFKHHQLRTMKSYF +NQNP
Sbjct: 155 ILHRGDLSSSMESLAYDSGA--ASPGS--VSSTRTKRMRTSFKHHQLRTMKSYFAVNQNP 210

Query: 61  DAKDLKQLAQKTGLSKRVLQ 80
           DAKDLKQLAQKTGLSKRVLQ
Sbjct: 211 DAKDLKQLAQKTGLSKRVLQ 230

Source: Cydia pomonella

Species: Cydia pomonella

Genus: Cydia

Family: Tortricidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota
>gi|328925124|dbj|BAK19077.1| apterous B alpha [Bombyx mori] Back     alignment and taxonomy information
>gi|328925126|dbj|BAK19078.1| apterous B beta [Bombyx mori] Back     alignment and taxonomy information
>gi|345487079|ref|XP_001599685.2| PREDICTED: LIM/homeobox protein Lhx9-like [Nasonia vitripennis] Back     alignment and taxonomy information
>gi|357622661|gb|EHJ74087.1| apterous [Danaus plexippus] Back     alignment and taxonomy information
>gi|225543484|ref|NP_001139388.1| apterous [Tribolium castaneum] gi|224459214|gb|ACN43342.1| apterous b [Tribolium castaneum] Back     alignment and taxonomy information
>gi|270004906|gb|EFA01354.1| apterous 2 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|340721020|ref|XP_003398925.1| PREDICTED: LIM/homeobox protein Lhx9-like [Bombus terrestris] Back     alignment and taxonomy information
>gi|350404759|ref|XP_003487211.1| PREDICTED: LIM/homeobox protein Lhx9-like [Bombus impatiens] Back     alignment and taxonomy information
>gi|328787166|ref|XP_003250891.1| PREDICTED: LIM/homeobox protein Lhx9-like [Apis mellifera] 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 ?
Query80
UNIPROTKB|E1BXQ7395 E1BXQ7 "Uncharacterized protei 0.625 0.126 0.9 4.6e-19
UNIPROTKB|F1P3H6413 F1P3H6 "Uncharacterized protei 0.625 0.121 0.9 5.6e-19
UNIPROTKB|E1BSF2330 LHX9 "LIM/homeobox protein Lhx 0.6 0.145 0.916 6.5e-19
UNIPROTKB|E2R2S6330 LHX9 "Uncharacterized protein" 0.6 0.145 0.916 6.5e-19
UNIPROTKB|H0YL54336 LHX9 "LIM/homeobox protein Lhx 0.6 0.142 0.916 6.5e-19
UNIPROTKB|Q68EY3331 lhx9 "LIM/homeobox protein Lhx 0.6 0.145 0.916 6.5e-19
UNIPROTKB|E1BM14406 LHX2 "Uncharacterized protein" 0.625 0.123 0.9 8.8e-19
UNIPROTKB|E2RPC3406 LHX2 "Uncharacterized protein" 0.625 0.123 0.9 8.8e-19
UNIPROTKB|P50458406 LHX2 "LIM/homeobox protein Lhx 0.625 0.123 0.9 8.8e-19
UNIPROTKB|C4TJC6406 Lhx2 "LIM homeobox protein 2" 0.625 0.123 0.9 8.8e-19
UNIPROTKB|E1BXQ7 E1BXQ7 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
 Score = 232 (86.7 bits), Expect = 4.6e-19, P = 4.6e-19
 Identities = 45/50 (90%), Positives = 48/50 (96%)

Query:    31 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80
             S+Q+TKRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct:   251 SNQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 300
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0008270 "zinc ion binding" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=IEA
UNIPROTKB|F1P3H6 F1P3H6 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E1BSF2 LHX9 "LIM/homeobox protein Lhx9" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2R2S6 LHX9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|H0YL54 LHX9 "LIM/homeobox protein Lhx9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q68EY3 lhx9 "LIM/homeobox protein Lhx9" [Xenopus laevis (taxid:8355)] Back     alignment and assigned GO terms
UNIPROTKB|E1BM14 LHX2 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2RPC3 LHX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P50458 LHX2 "LIM/homeobox protein Lhx2" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|C4TJC6 Lhx2 "LIM homeobox protein 2" [Sus scrofa (taxid:9823)] 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) ?
Q9Z0S2LHX2_MOUSENo assigned EC number0.90.6250.1231yesN/A
Q68EY3LHX9_XENLANo assigned EC number0.91660.60.1450N/AN/A
P50458LHX2_HUMANNo assigned EC number0.90.6250.1231yesN/A
P29673APTE_DROMENo assigned EC number0.83630.68750.1172yesN/A
A0JNI8LHX9_BOVINNo assigned EC number0.91660.60.1209noN/A
Q9NQ69LHX9_HUMANNo assigned EC number0.91660.60.1209noN/A
Q80W90LHX9_RATNo assigned EC number0.91660.60.1237noN/A
Q9WUH2LHX9_MOUSENo assigned EC number0.91660.60.1209noN/A
Q1LWV4LHX9_DANRENo assigned EC number0.91660.60.1212noN/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 ?
Query80
pfam0004657 pfam00046, Homeobox, Homeobox domain 3e-13
smart0038957 smart00389, HOX, Homeodomain 4e-12
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 3e-11
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 57.5 bits (140), Expect = 3e-13
 Identities = 16/45 (35%), Positives = 30/45 (66%)

Query: 36 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80
          +R RT+F   QL  ++  F  N+ P A++ ++LA+K GL++R ++
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45

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 80
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.42
KOG0488|consensus309 99.42
KOG0484|consensus125 99.35
KOG2251|consensus 228 99.34
KOG0842|consensus 307 99.33
KOG0850|consensus245 99.32
KOG0843|consensus197 99.29
KOG0489|consensus261 99.27
KOG0485|consensus 268 99.18
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.18
KOG0494|consensus 332 99.14
KOG0487|consensus308 99.09
KOG0486|consensus 351 99.07
KOG0493|consensus342 99.04
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.04
KOG0492|consensus246 99.02
cd0008659 homeodomain Homeodomain; DNA binding domains invol 98.94
KOG0491|consensus194 98.86
KOG0848|consensus317 98.81
KOG0844|consensus 408 98.72
KOG3802|consensus398 98.64
KOG0490|consensus 235 98.59
COG5576156 Homeodomain-containing transcription factor [Trans 98.58
KOG0849|consensus 354 98.56
KOG4577|consensus 383 98.06
KOG2252|consensus558 97.89
KOG0483|consensus 198 97.79
KOG0847|consensus288 97.42
KOG1168|consensus385 97.1
KOG0774|consensus334 96.91
KOG0775|consensus304 96.77
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 96.77
KOG0490|consensus235 96.64
KOG1146|consensus 1406 95.44
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 94.11
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 93.28
COG3413215 Predicted DNA binding protein [General function pr 89.82
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 82.3
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information 
Probab=99.42  E-value=5.1e-13  Score=68.15  Aligned_cols=45  Identities=20%  Similarity=0.434  Sum_probs=43.4

Q ss_pred             CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCccccC
Q psy4349          36 KRMRTSFKHHQLRTMKSYFNINQN----PDAKDLKQLAQKTGLSKRVLQ   80 (80)
Q Consensus        36 rr~Rt~~t~~ql~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~Vk   80 (80)
                      +|.||.||..|+..|+..|+.++|    |+...+.+||..|||++.+||
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK   50 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK   50 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence            689999999999999999999999    999999999999999999886

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
>KOG0488|consensus Back     alignment and domain information
>KOG0484|consensus Back     alignment and domain information
>KOG2251|consensus Back     alignment and domain information
>KOG0842|consensus Back     alignment and domain information
>KOG0850|consensus Back     alignment and domain information
>KOG0843|consensus Back     alignment and domain information
>KOG0489|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
>KOG0494|consensus Back     alignment and domain information
>KOG0487|consensus Back     alignment and domain information
>KOG0486|consensus Back     alignment and domain information
>KOG0493|consensus Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG0492|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
>KOG0491|consensus Back     alignment and domain information
>KOG0848|consensus Back     alignment and domain information
>KOG0844|consensus Back     alignment and domain information
>KOG3802|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>KOG4577|consensus Back     alignment and domain information
>KOG2252|consensus Back     alignment and domain information
>KOG0483|consensus Back     alignment and domain information
>KOG0847|consensus Back     alignment and domain information
>KOG1168|consensus Back     alignment and domain information
>KOG0774|consensus Back     alignment and domain information
>KOG0775|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
>KOG0490|consensus Back     alignment and domain information
>KOG1146|consensus 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
>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
>COG3413 Predicted DNA binding protein [General function prediction only] Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query80
2dmq_A80 Solution Structure Of The Homeobox Domain Of LimHOM 8e-19
2da1_A70 Solution Structure Of The First Homeobox Domain Of 6e-06
1bw5_A66 The Nmr Solution Structure Of The Homeodomain Of Th 5e-04
2da3_A80 Solution Structure Of The Third Homeobox Domain Of 6e-04
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX Protein Lhx9 Length = 80 Back     alignment and structure 
Iteration: 1

 Score = 88.6 bits (218), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 42/45 (93%), Positives = 43/45 (95%)
Query: 36 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80
          KRMRTSFKHHQLRTMKSYF IN NPDAKDLKQLAQKTGL+KRVLQ
Sbjct: 8  KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 70 Back     alignment and structure
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66 Back     alignment and structure
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At- Binding Transcription Factor 1 (Atbf1) Length = 80 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 ?
Query80
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 1e-20
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-19
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 1e-18
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 6e-18
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 3e-17
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 1e-15
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 2e-14
1e3o_C160 Octamer-binding transcription factor 1; transcript 1e-13
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 1e-12
2xsd_C164 POU domain, class 3, transcription factor 1; trans 1e-11
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 2e-11
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 6e-11
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 1e-10
3d1n_I151 POU domain, class 6, transcription factor 1; prote 2e-09
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 9e-09
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 3e-08
2e19_A64 Transcription factor 8; homeobox domain, structura 3e-08
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 7e-08
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 7e-08
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 8e-08
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 1e-07
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 2e-05
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 3e-05
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 5e-05
1uhs_A72 HOP, homeodomain only protein; structural genomics 7e-05
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 2e-04
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 3e-04
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 3e-04
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 4e-04
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 4e-04
1wh5_A80 ZF-HD homeobox family protein; structural genomics 5e-04
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 5e-04
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 7e-04
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 9e-04
>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
 Score = 76.4 bits (188), Expect = 1e-20
 Identities = 24/62 (38%), Positives = 35/62 (56%)

Query: 19 GAGNSSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRV 78
          G+  SS G+G    QR KR+RT+    QL  +   + ++ NP  K L  +A + GL KRV
Sbjct: 1  GSSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRV 60

Query: 79 LQ 80
          +Q
Sbjct: 61 VQ 62
>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
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66 Back     alignment and structure
>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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 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
>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
>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
>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
>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
>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
>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64 Back     alignment and structure
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 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} Length = 71 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
>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
>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
>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
>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
>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
>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
>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
>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
>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 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
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Length = 87 Back     alignment and structure
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query80
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.59
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.56
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.56
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.55
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.54
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.52
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.5
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.5
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.5
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.5
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.48
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.48
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.47
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.47
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.46
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.46
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.46
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.45
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.45
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.44
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.44
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.44
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.43
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.43
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.43
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.42
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.42
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.42
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.41
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.41
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.41
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.4
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.4
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.39
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.39
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.38
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.37
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.36
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.35
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.34
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.34
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.33
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.32
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.31
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.31
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.3
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.29
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.29
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.28
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.28
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.28
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.27
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.26
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.26
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.25
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.24
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.24
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.21
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.2
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.19
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.18
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.18
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.17
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.15
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.1
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.1
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.03
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.03
2e19_A64 Transcription factor 8; homeobox domain, structura 99.0
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 98.96
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 98.94
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 98.91
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 98.77
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 98.77
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 98.54
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 98.44
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 98.22
2rgt_A169 Fusion of LIM/homeobox protein LHX3, linker, INSU 92.49
>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
Probab=99.59  E-value=5.3e-15  Score=79.21  Aligned_cols=52  Identities=25%  Similarity=0.320  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349          29 VHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ   80 (80)
Q Consensus        29 ~~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk   80 (80)
                      +....+.++.||.||..|+..|+..|..++||+..++.+||..++|++.+|+
T Consensus        11 ~~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~   62 (80)
T 2dmt_A           11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK   62 (80)
T ss_dssp             CCCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHee
Confidence            3445677889999999999999999999999999999999999999999885
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Back     alignment and structure
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* 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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} 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
>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
>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
>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
>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
>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
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Back     alignment and structure
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Back     alignment and structure
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} 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
>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
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A 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
>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
>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
>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
>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
>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
>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
>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
>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
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>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
>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
>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
>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
>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A 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 80
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 8e-10
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 1e-09
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 1e-08
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 3e-08
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 3e-08
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 4e-08
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 6e-08
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 8e-08
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 1e-07
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 2e-07
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 2e-07
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 2e-07
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 5e-07
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 7e-07
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 9e-07
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 1e-06
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 2e-06
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 4e-06
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 5e-06
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 6e-06
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 7e-06
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 8e-06
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 9e-06
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 3e-05
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 8e-05
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 1e-04
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 1e-04
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 4e-04
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 4e-04
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 0.004
>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 = 47.9 bits (114), Expect = 8e-10
 Identities = 10/58 (17%), Positives = 26/58 (44%)

Query: 23 SSPGSGVHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80
          ++P +     + T++ R  +  HQ   ++  F  N         ++A+   L++R ++
Sbjct: 1  NNPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 58
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 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
>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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 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
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 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
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 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
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57 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
>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
>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
>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
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78 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
>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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query80
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.56
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.55
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.55
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.55
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.54
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.53
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.52
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.51
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.51
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.51
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.51
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.49
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.46
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.46
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.44
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.44
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.43
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.43
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.39
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.36
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.35
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.35
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.29
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.26
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.14
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.09
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.08
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.02
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 98.97
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 98.81
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 98.72
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 98.71
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 86.11
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} 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]

Probab=99.56  E-value=3.9e-15  Score=78.03  Aligned_cols=49  Identities=18%  Similarity=0.280  Sum_probs=45.2

Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349          32 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ   80 (80)
Q Consensus        32 ~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk   80 (80)
                      ....++.||.||..|+..|+..|..++||+...+..||..+||++.+|+
T Consensus        10 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~   58 (77)
T d1pufa_          10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK   58 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHH
T ss_pred             cCcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhh
Confidence            3445778999999999999999999999999999999999999999885
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} 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
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d1fjla_ a.4.1.1 (A:) Paired 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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} 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
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {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
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure