Citrus Sinensis ID: 040593

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
MALTLSTSICTSTSRAVHRLSPSQYLRLFPGHHRKPTNLLLPRHPPTRFTLAFSRRRNNNPVTISSSKKKKKSLPRKDIKDSDEEDDPFEALFSLLEEDLKNDDSTIDDDDEEIDEEDLDKLATELAEALGDVDMDMSDTATDGTESDNNEAHKEDGEDEEEEEEREVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRKPFQRSDPKTVFSG
cccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccccccccccc
ccEEEEccEccccccEEEEcccccccccccccccccccccccccccccEEEEEEccccccccEEEccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHccccccHHHHHHcccccccccccccccccccccccccHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccccccccccEccc
maltlstsictstsravhrlspsqylrlfpghhrkptnlllprhpptrftLAFSrrrnnnpvtissskkkkkslprkdikdsdeeddPFEALFSLLEEdlknddstiddddeeideEDLDKLATELAEALgdvdmdmsdtatdgtesdnneahkedgedeeEEEEREVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEmlgdpppnllmlsatlpdkptptvlvnevkhsepivaettvhavepkskveepvhdrQHRWSAQKRLKKVQVKTLEMVYrrskrptdaMISSIVQvtnlprrrIVKWFEdkraeegvpecrkpfqrsdpktvfsg
maltlstsictstsravhrlspsqYLRLFPGHhrkptnlllprhpptrftlafsrrrnnnpvtissskkkkkslprkdikdsdeeddPFEALFSLLeedlknddstiddddeeidEEDLDKLATELAEalgdvdmdMSDTatdgtesdnneahkedgedeeeeeEREVRLKNWQLRKLAYalktgrrkvsvKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHsepivaettvhavepkskveepvhdrqhrwsaqkrlkkvqvktlemvyrrskrptdamissivqvtnlprrriVKWFedkraeegvpecrkpfqrsdpktvfsg
MAltlstsictstsRAVHRLSPSQYLRLFPGHHRKPTNLLLPRHPPTRFTLAFSRRRNNNPVTIssskkkkksLPRKDIKDSDEEDDPFEALFSLLEEdlknddstiddddeeideedldkLATELAEALGDVDMDMSDTATDGTESDNNEAHKedgedeeeeeereVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRKPFQRSDPKTVFSG
************************YLRLFPG******************************************************************************************************************************************LKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSAT********VLVN******************************************VQVKTLEMVYRR****TDAMISSIVQVTNLPRRRIVKWFE**************************
*******************LSPSQYLRLFPGHHRKPTNLLLPRHPPTRF**************************************PFEALFSLLEED**************IDEEDLDKLATELAEALGDVDMDMSDTA*******************************WQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP******************************************************************VKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFED*************************
MALTLSTSICTSTSRAVHRLSPSQYLRLFPGHHRKPTNLLLPRHPPTRFTLAFSRRRNNN**************************DPFEALFSLLEEDLKNDDSTIDDDDEEIDEEDLDKLATELAEALGDVDMDMSDT*****************************LKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKS*****************RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRKPF***********
*ALTLSTSICTSTSRAVHRLSPSQYLRLFPGHHRKPTNLLLPRHPPTRFTLAFSRR*****************************DDPFEALFSLLEEDLKND********EEIDEEDLDKLATELAEALGDVD*******************************REVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATL*************************************V***QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEE********************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MALTLSTSICTSTSRAVHRLSPSQYLRLFPGHHRKPTNLLLPRHPPTRFTLAFSRRRNNNPVTISSSKKKKKSLPRKDIKDSDEEDDPFEALFSLLEEDLKNDDSTIDDDDEEIDEEDLDKLATELAEALGDVDMDMSDTATDGTESDNNEAHKEDGEDEEEEEEREVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRKPFQRSDPKTVFSG
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query342
296082012342 unnamed protein product [Vitis vinifera] 0.921 0.921 0.602 4e-89
359475806402 PREDICTED: uncharacterized protein LOC10 0.909 0.773 0.579 9e-85
224089192340 predicted protein [Populus trichocarpa] 0.891 0.897 0.579 9e-80
147867261282 hypothetical protein VITISV_036369 [Viti 0.730 0.886 0.610 6e-74
297811239352 hypothetical protein ARALYDRAFT_487959 [ 0.880 0.855 0.551 2e-71
255548966338 conserved hypothetical protein [Ricinus 0.961 0.973 0.518 8e-69
356509922322 PREDICTED: uncharacterized protein LOC10 0.745 0.791 0.558 8e-68
449437388324 PREDICTED: uncharacterized protein LOC10 0.824 0.870 0.519 5e-65
449503534345 PREDICTED: uncharacterized protein LOC10 0.868 0.860 0.515 8e-65
356515458338 PREDICTED: uncharacterized protein LOC10 0.923 0.934 0.482 4e-63
>gi|296082012|emb|CBI21017.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
 Score =  334 bits (857), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 200/332 (60%), Positives = 243/332 (73%), Gaps = 17/332 (5%)

Query: 20  LSPSQYLRLFPGHHRKPT-NLLLPRHPPTRFTLAFSRRR-NNNPVTISSSKKKKKSLPRK 77
           LS S   RLF     +PT NL+LP H  +R  LAFSRRR +N+PV  S   KK  +    
Sbjct: 17  LSASHDQRLFSAA--QPTSNLILPHHCLSRSVLAFSRRRKSNSPVQSSKKNKKSSAHNNA 74

Query: 78  DIKDSDEEDDPFEALFSLLEEDLKNDDSTIDDDDEEIDEEDLDKLATELAEALGDVD--M 135
           + +D+D ++D FEALF+ LEEDLKND  +IDD+DEEI EEDL +L  EL EALGD D  +
Sbjct: 75  E-EDADLDEDAFEALFNQLEEDLKNDSPSIDDNDEEISEEDLARLERELEEALGDDDELL 133

Query: 136 DMSDTATDGTESDNNEAHKEDGEDEEEEEEREVRLKNWQLRKLAYALKTGRRKVSVKSLA 195
            M ++ TD  ES+N+    E    ++E+EER V+LKNWQLR+LA ALKTGRRK S+KSLA
Sbjct: 134 GMFNSITDEIESNNDAEEVE----DDEDEERPVKLKNWQLRRLASALKTGRRKTSIKSLA 189

Query: 196 AELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVE--- 252
           AELCLDRAVVLE+L +PPPNLL++SA LPDKP PT+ V E +  E +  +TT  AVE   
Sbjct: 190 AELCLDRAVVLELLREPPPNLLLMSAALPDKPVPTITVPETEPVEAVPLDTTRGAVEAAE 249

Query: 253 ---PKSKVEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRR 309
              P+ K + PVH  Q RWSAQKRLKKVQV+TLE VYRR+KRPT+AMISSIV VTNLPR+
Sbjct: 250 PAEPEVKGKVPVHVMQSRWSAQKRLKKVQVETLERVYRRTKRPTNAMISSIVHVTNLPRK 309

Query: 310 RIVKWFEDKRAEEGVPECRKPFQRSDPKTVFS 341
           R+VKWFEDKR E+GVPE R PFQRS  +TVFS
Sbjct: 310 RVVKWFEDKRTEDGVPEHRLPFQRSTSETVFS 341

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359475806|ref|XP_002285025.2| PREDICTED: uncharacterized protein LOC100254226 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224089192|ref|XP_002308655.1| predicted protein [Populus trichocarpa] gi|222854631|gb|EEE92178.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|147867261|emb|CAN81198.1| hypothetical protein VITISV_036369 [Vitis vinifera] Back     alignment and taxonomy information
>gi|297811239|ref|XP_002873503.1| hypothetical protein ARALYDRAFT_487959 [Arabidopsis lyrata subsp. lyrata] gi|297319340|gb|EFH49762.1| hypothetical protein ARALYDRAFT_487959 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|255548966|ref|XP_002515539.1| conserved hypothetical protein [Ricinus communis] gi|223545483|gb|EEF46988.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|356509922|ref|XP_003523691.1| PREDICTED: uncharacterized protein LOC100784216 [Glycine max] Back     alignment and taxonomy information
>gi|449437388|ref|XP_004136474.1| PREDICTED: uncharacterized protein LOC101218040 [Cucumis sativus] Back     alignment and taxonomy information
>gi|449503534|ref|XP_004162050.1| PREDICTED: uncharacterized protein LOC101225231 [Cucumis sativus] Back     alignment and taxonomy information
>gi|356515458|ref|XP_003526417.1| PREDICTED: uncharacterized protein LOC100798718 [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query342
TAIR|locus:2148012354 OCP3 "overexpressor of cationi 0.871 0.841 0.472 8.8e-63
TAIR|locus:2148012 OCP3 "overexpressor of cationic peroxidase 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 154/326 (47%), Positives = 191/326 (58%)

Query:    28 LFPGHHRKPTNLLLPRHPPTRFTLAFSRRRNNNPVTIXXXXXXXXXLPRKDIKDSD---- 83
             LF   +  P  L LP   P+R  L F+R +N     +           +K +  +D    
Sbjct:    33 LFRNRNASPCGLSLPILNPSRSVLVFARGKNRKGF-VSSSSSSPKKNKKKSLDGADNGGG 91

Query:    84 -EEDDPFEALFSLLEEXXXXXXXXXXXXXXXXXXXXXXXLATELAEALG---DVD-MDMS 138
              EE+DPFEALF+LLEE                       LA ELA ALG   DVD +D+ 
Sbjct:    92 EEEEDPFEALFNLLEEDLKNDNSDDEEISEEELEA----LADELARALGVGDDVDDIDLF 147

Query:   139 DTAT-------DGTESDNNEAHKXXXXXXXXXXXXXVRLKNWQLRKLAYALKTGRRKVSV 191
              + T       D  + DN++                 +LKNWQL++LAYALK GRRK S+
Sbjct:   148 GSVTGDVDVDVDNDDDDNDDDDNDDDDDDSEEDERPTKLKNWQLKRLAYALKAGRRKTSI 207

Query:   192 KSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPD-KPTPTVLVNEVKHSEPIV---AETT 247
             K+LAAE+CLDRA VLE+L DPPP LLMLSATLPD KP      N      P+    AE  
Sbjct:   208 KNLAAEVCLDRAYVLELLRDPPPKLLMLSATLPDEKPPVAAPENSSPDPSPVESLSAEDV 267

Query:   248 VHAVEPKSKV-EEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNL 306
             V  VEPK KV +E VH  Q RWSAQKR+KK  ++TLE VYRRSKRPT+A++SSIVQVTNL
Sbjct:   268 V--VEPKEKVKDEAVHVMQQRWSAQKRVKKAHIETLEKVYRRSKRPTNAVVSSIVQVTNL 325

Query:   307 PRRRIVKWFEDKRAEEGVPECRKPFQ 332
             PR+R++KWFEDKRAE+GVP+ R P+Q
Sbjct:   326 PRKRVLKWFEDKRAEDGVPDKRAPYQ 351


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.132   0.383    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      342       285   0.00085  115 3  11 22  0.39    34
                                                     33  0.42    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  602 (64 KB)
  Total size of DFA:  202 KB (2113 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.95u 0.13s 23.08t   Elapsed:  00:00:01
  Total cpu time:  22.95u 0.13s 23.08t   Elapsed:  00:00:01
  Start:  Sat May 11 02:34:52 2013   End:  Sat May 11 02:34:53 2013
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0009507 "chloroplast" evidence=ISM
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=IDA
GO:0006952 "defense response" evidence=IMP
GO:0009867 "jasmonic acid mediated signaling pathway" evidence=IMP
GO:0009414 "response to water deprivation" evidence=IMP
GO:0009737 "response to abscisic acid stimulus" evidence=IEP
GO:0010118 "stomatal movement" evidence=IMP
GO:0050832 "defense response to fungus" evidence=IMP

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query342
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 3e-07
smart0038957 smart00389, HOX, Homeodomain 6e-07
COG3343175 COG3343, RpoE, DNA-directed RNA polymerase, delta 7e-06
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 3e-05
pfam0004657 pfam00046, Homeobox, Homeobox domain 2e-04
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 6e-04
pfam05764238 pfam05764, YL1, YL1 nuclear protein 8e-04
pfam11705221 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polym 0.001
COG5414392 COG5414, COG5414, TATA-binding protein-associated 0.002
pfam04147 809 pfam04147, Nop14, Nop14-like family 0.003
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information 
 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 11/53 (20%), Positives = 25/53 (47%)

Query: 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320
              + R    Q++ LE  + ++  P+      + +   L  R++  WF+++RA
Sbjct: 1   RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRA 53

Length = 59
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|225880 COG3343, RpoE, DNA-directed RNA polymerase, delta subunit [Transcription] Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein Back     alignment and domain information
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit Rpc31 Back     alignment and domain information
>gnl|CDD|227701 COG5414, COG5414, TATA-binding protein-associated factor [Transcription] Back     alignment and domain information
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 342
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.81
KOG2251 228 consensus Homeobox transcription factor [Transcrip 99.76
KOG0494 332 consensus Transcription factor CHX10 and related H 99.72
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.64
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.58
KOG0489261 consensus Transcription factor zerknullt and relat 99.58
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.55
KOG0490235 consensus Transcription factor, contains HOX domai 99.53
KOG0488309 consensus Transcription factor BarH and related HO 99.53
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.53
KOG0843197 consensus Transcription factor EMX1 and related HO 99.48
KOG0486 351 consensus Transcription factor PTX1, contains HOX 99.45
KOG4577 383 consensus Transcription factor LIM3, contains LIM 99.44
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.42
COG5576156 Homeodomain-containing transcription factor [Trans 99.32
KOG0849 354 consensus Transcription factor PRD and related pro 99.32
KOG0844 408 consensus Transcription factor EVX1, contains HOX 99.28
KOG0493342 consensus Transcription factor Engrailed, contains 99.25
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.23
KOG0483198 consensus Transcription factor HEX, contains HOX a 99.21
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.18
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.18
KOG0848317 consensus Transcription factor Caudal, contains HO 99.11
KOG0850245 consensus Transcription factor DLX and related pro 99.1
KOG0847288 consensus Transcription factor, contains HOX domai 99.03
KOG0491194 consensus Transcription factor BSH, contains HOX d 98.97
KOG3802398 consensus Transcription factor OCT-1, contains POU 98.9
KOG0490235 consensus Transcription factor, contains HOX domai 98.62
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.04
KOG0775304 consensus Transcription factor SIX and related HOX 98.01
KOG2252558 consensus CCAAT displacement protein and related h 97.83
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 97.68
KOG1146 1406 consensus Homeobox protein [General function predi 97.2
KOG0774334 consensus Transcription factor PBX and related HOX 97.18
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 96.12
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 95.84
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 95.82
COG3413215 Predicted DNA binding protein [General function pr 95.2
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 95.05
KOG0773342 consensus Transcription factor MEIS1 and related H 94.91
PF04931784 DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070 93.35
PF0004657 Homeobox: Homeobox domain not present here.; Inter 90.57
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 90.0
PF04931784 DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070 89.89
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 89.52
KOG18321516 consensus HIV-1 Vpr-binding protein [Cell cycle co 87.95
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 87.87
PF1351852 HTH_28: Helix-turn-helix domain 86.61
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 86.35
PF13551112 HTH_29: Winged helix-turn helix 85.98
cd0008659 homeodomain Homeodomain; DNA binding domains invol 84.37
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 82.75
COG5414392 TATA-binding protein-associated factor [Transcript 80.87
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 80.45
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] Back     alignment and domain information 
Probab=99.81  E-value=6.4e-21  Score=161.35  Aligned_cols=68  Identities=21%  Similarity=0.358  Sum_probs=61.4

Q ss_pred             CCccccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593          260 PVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC  327 (342)
Q Consensus       260 P~~~~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~  327 (342)
                      .++...++.+-||+||..||.+||++|.-|||||+++||+||.++.|++.||||||||||||.+--++
T Consensus        10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr   77 (125)
T KOG0484|consen   10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER   77 (125)
T ss_pred             ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence            34555677899999999999999999999999999999999999999999999999999999765443

>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only] 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
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>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
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A 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
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription] Back     alignment and domain information
>COG3413 Predicted DNA binding protein [General function prediction only] Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>PF13518 HTH_28: Helix-turn-helix domain 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
>PF13551 HTH_29: Winged helix-turn helix 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
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>COG5414 TATA-binding protein-associated factor [Transcription] Back     alignment and domain information
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query342
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 3e-11
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-11
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 2e-10
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 5e-09
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 1e-07
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 2e-06
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 6e-06
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 3e-05
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 4e-05
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 5e-05
2xsd_C164 POU domain, class 3, transcription factor 1; trans 1e-04
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 1e-04
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 2e-04
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-04
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 3e-04
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 4e-04
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 5e-04
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 6e-04
>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
 Score = 57.5 bits (139), Expect = 3e-11
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 265 QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320
            H     ++  K Q+  L+  + +S+ P DA +  +++VT L R  I KWF D R 
Sbjct: 2   AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY 57
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76 Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75 Back     alignment and structure
>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
>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
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164 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
>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
>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
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query342
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.79
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.79
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.79
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.78
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.78
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.77
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.77
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.77
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.77
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.77
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.77
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.77
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.77
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.77
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.77
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.77
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.76
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.76
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.76
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.76
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.76
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.75
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.75
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.75
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.75
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.75
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.75
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.75
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.75
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.75
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.75
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.75
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.75
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.75
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.75
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.74
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.74
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.74
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.74
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.74
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.73
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.73
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.73
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.73
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.73
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.73
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.72
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.71
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.71
2e19_A64 Transcription factor 8; homeobox domain, structura 99.71
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.7
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.7
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.7
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.69
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.68
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.67
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.67
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.67
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.67
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.67
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.67
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.67
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.66
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.66
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.66
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.65
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.64
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.64
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.63
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.61
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.6
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.59
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.53
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.53
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.5
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.49
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.18
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 97.95
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 93.59
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 93.01
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 92.77
1neq_A74 DNA-binding protein NER; NMR {Enterobacteria phage 90.95
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 89.78
2k27_A159 Paired box protein PAX-8; paired domain, solution 89.69
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 88.89
2heo_A67 Z-DNA binding protein 1; protein DLM1-Z-DNA comple 85.47
1u78_A141 TC3 transposase, transposable element TC3 transpos 84.86
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 84.19
2x48_A55 CAG38821; archeal virus, viral protein; 2.60A {Sul 82.14
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 80.98
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 80.97
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 80.56
>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
Probab=99.79  E-value=1.9e-19  Score=137.46  Aligned_cols=59  Identities=15%  Similarity=0.339  Sum_probs=56.2

Q ss_pred             ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593          266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV  324 (342)
Q Consensus       266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v  324 (342)
                      .....||.||..||..||.+|..++||+...|+.||..|||++.+|+|||||||+|++-
T Consensus        21 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk   79 (84)
T 2kt0_A           21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR   79 (84)
T ss_dssp             CSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence            45679999999999999999999999999999999999999999999999999999874
>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
>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
>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
>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
>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
>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
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; 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
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} 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
>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
>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
>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
>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
>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
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; 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
>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
>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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Back     alignment and structure
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_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
>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
>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
>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
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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_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
>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
>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
>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
>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
>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
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Back     alignment and structure
>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
>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
>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
>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
>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
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2 Back     alignment and structure
>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
>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A 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
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A Back     alignment and structure
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Back     alignment and structure
>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
>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid} 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
>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

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 342
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 3e-05
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 3e-05
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 5e-05
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 7e-05
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 7e-05
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 1e-04
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 1e-04
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 3e-04
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 3e-04
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 3e-04
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 3e-04
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 4e-04
d2ecca176 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H 5e-04
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 5e-04
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 7e-04
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 8e-04
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 9e-04
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 0.001
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 0.001
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 0.002
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 0.003
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 0.003
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure

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

 Score = 39.0 bits (91), Expect = 3e-05
 Identities = 12/51 (23%), Positives = 22/51 (43%)

Query: 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320
            Q R    Q   LE  +   K  +      + ++  L  R++  WF+++RA
Sbjct: 3   GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA 53
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 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
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 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
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 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
>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
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 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
>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
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 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 ?
Query342
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.82
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.81
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.81
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.8
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.8
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.78
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.77
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.77
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.77
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.77
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.76
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.76
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.76
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.75
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.75
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.75
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.75
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.74
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.74
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.74
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.73
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.72
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.72
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.71
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.71
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.7
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.63
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.62
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.61
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.6
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.55
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.47
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 93.67
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 89.43
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 84.85
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 83.87
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 82.55
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 81.49
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 80.5
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 80.26
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=5.5e-21  Score=140.06  Aligned_cols=56  Identities=29%  Similarity=0.399  Sum_probs=53.9

Q ss_pred             ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593          268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG  323 (342)
Q Consensus       268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~  323 (342)
                      ...||.||.+|++.||.+|+.++||+...|+.||..+||++.+|+|||||||+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~k   57 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK   57 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhcc
Confidence            45799999999999999999999999999999999999999999999999999975
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} 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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>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
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {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
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} 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
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>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