Psyllid ID: psy5355

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------
NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQVKS
cccccccccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHccHHHHHHHcHHHHHHcc
cccccccccccccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHccccccEEEEccccHHHHHHHccccHccccc
nnsdkdakkkhtrptfsgqQIFALEKTFEQTKYLAGPERAKLAYALGmtesqvkvtgpERAKLAYALGmtesqvks
nnsdkdakkkhtrptfsgqqifALEKTFEQTKYLAGPERAKLAYALGMtesqvkvtgpERAKLAyalgmtesqvks
NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQVKS
*******************QIFALEKTFEQTKYLAGPERAKLAYALGMT***************************
****************SGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERA***************
**************TFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQVKS
***************FSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKL**AL*********
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iiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
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NNSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGPERAKLAYALGMTESQVKS
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 ?
Query76 2.2.26 [Sep-21-2011]
Q60554364 Homeobox protein Nkx-6.1 N/A N/A 0.684 0.142 0.923 8e-23
P78426367 Homeobox protein Nkx-6.1 yes N/A 0.684 0.141 0.923 8e-23
O35762365 Homeobox protein Nkx-6.1 yes N/A 0.684 0.142 0.923 8e-23
Q99MA9365 Homeobox protein Nkx-6.1 yes N/A 0.684 0.142 0.923 9e-23
Q9C056277 Homeobox protein Nkx-6.2 no N/A 0.684 0.187 0.923 2e-22
A6NJ46265 Homeobox protein Nkx-6.3 no N/A 0.697 0.2 0.867 1e-20
Q3UHX8262 Homeobox protein Nkx-6.3 no N/A 0.697 0.202 0.867 1e-20
A5YC49254 Homeobox protein Nkx-6.3 N/A N/A 0.723 0.216 0.763 7e-20
P78367333 Homeobox protein Nkx-3.2 no N/A 0.631 0.144 0.520 2e-08
P97503333 Homeobox protein Nkx-3.2 no N/A 0.631 0.144 0.520 3e-08
>sp|Q60554|NKX61_MESAU Homeobox protein Nkx-6.1 OS=Mesocricetus auratus GN=NKX6-1 PE=1 SV=1 Back     alignment and function desciption
 Score =  105 bits (262), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 48/52 (92%), Positives = 51/52 (98%)

Query: 4   DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
           DKD K+KHTRPTFSGQQIFALEKTFEQTKYLAGPERA+LAY+LGMTESQVKV
Sbjct: 231 DKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAYSLGMTESQVKV 282
Together with NKX2-2 and IRX3 acts to restrict the generation of motor neurons to the appropriate region of the neural tube. Belongs to the class II proteins of neuronal progenitor factors, which are induced by SHH signals (By similarity). Transcription factor which binds to specific A/T-rich DNA sequences in the promoter regions of a number of genes. Involved in transcriptional regulation in islet beta cells. Binds to the insulin promoter and is involved in regulation of the insulin gene.
Mesocricetus auratus (taxid: 10036)
>sp|P78426|NKX61_HUMAN Homeobox protein Nkx-6.1 OS=Homo sapiens GN=NKX6-1 PE=2 SV=2 Back     alignment and function description
>sp|O35762|NKX61_RAT Homeobox protein Nkx-6.1 OS=Rattus norvegicus GN=Nkx6-1 PE=2 SV=1 Back     alignment and function description
>sp|Q99MA9|NKX61_MOUSE Homeobox protein Nkx-6.1 OS=Mus musculus GN=Nkx6-1 PE=1 SV=1 Back     alignment and function description
>sp|Q9C056|NKX62_HUMAN Homeobox protein Nkx-6.2 OS=Homo sapiens GN=NKX6-2 PE=2 SV=2 Back     alignment and function description
>sp|A6NJ46|NKX63_HUMAN Homeobox protein Nkx-6.3 OS=Homo sapiens GN=NKX6-3 PE=2 SV=1 Back     alignment and function description
>sp|Q3UHX8|NKX63_MOUSE Homeobox protein Nkx-6.3 OS=Mus musculus GN=Nkx6-3 PE=2 SV=1 Back     alignment and function description
>sp|A5YC49|NKX63_XENLA Homeobox protein Nkx-6.3 OS=Xenopus laevis GN=nkx6-3 PE=2 SV=1 Back     alignment and function description
>sp|P78367|NKX32_HUMAN Homeobox protein Nkx-3.2 OS=Homo sapiens GN=NKX3-2 PE=2 SV=2 Back     alignment and function description
>sp|P97503|NKX32_MOUSE Homeobox protein Nkx-3.2 OS=Mus musculus GN=Nkx3-2 PE=1 SV=2 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query76
350588013 340 PREDICTED: homeobox protein Nkx-6.1 [Sus 0.723 0.161 0.909 5e-23
149046766 316 rCG37924, isoform CRA_b [Rattus norvegic 0.723 0.174 0.909 5e-23
157104228 516 hypothetical protein AaeL_AAEL004033 [Ae 0.723 0.106 0.945 8e-23
347967851 622 AGAP002431-PA [Anopheles gambiae str. PE 0.684 0.083 0.980 1e-22
195019472 661 GH16803 [Drosophila grimshawi] gi|193898 0.697 0.080 0.962 2e-22
195378218 638 GJ11683 [Drosophila virilis] gi|19415503 0.710 0.084 0.944 2e-22
270015040 331 hypothetical protein TcasGA2_TC014200 [T 0.684 0.157 0.980 3e-22
189233719 295 PREDICTED: similar to HGTX CG13475-PA [T 0.684 0.176 0.980 4e-22
21358053 513 HGTX [Drosophila melanogaster] gi|696943 0.697 0.103 0.943 4e-22
19528431 480 RE18506p [Drosophila melanogaster] 0.697 0.110 0.943 4e-22
>gi|350588013|ref|XP_003129394.2| PREDICTED: homeobox protein Nkx-6.1 [Sus scrofa] Back     alignment and taxonomy information
 Score =  111 bits (278), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 50/55 (90%), Positives = 54/55 (98%)

Query: 4   DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP 58
           DKD K+KHTRPTFSGQQIFALEKTFEQTKYLAGPERA+LAY+LGMTESQVKV+GP
Sbjct: 232 DKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAYSLGMTESQVKVSGP 286

Source: Sus scrofa

Species: Sus scrofa

Genus: Sus

Family: Suidae

Order:

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota
>gi|149046766|gb|EDL99540.1| rCG37924, isoform CRA_b [Rattus norvegicus] Back     alignment and taxonomy information
>gi|157104228|ref|XP_001648311.1| hypothetical protein AaeL_AAEL004033 [Aedes aegypti] gi|108880426|gb|EAT44651.1| AAEL004033-PA [Aedes aegypti] Back     alignment and taxonomy information
>gi|347967851|ref|XP_563754.3| AGAP002431-PA [Anopheles gambiae str. PEST] gi|333468275|gb|EAL40928.3| AGAP002431-PA [Anopheles gambiae str. PEST] Back     alignment and taxonomy information
>gi|195019472|ref|XP_001984988.1| GH16803 [Drosophila grimshawi] gi|193898470|gb|EDV97336.1| GH16803 [Drosophila grimshawi] Back     alignment and taxonomy information
>gi|195378218|ref|XP_002047881.1| GJ11683 [Drosophila virilis] gi|194155039|gb|EDW70223.1| GJ11683 [Drosophila virilis] Back     alignment and taxonomy information
>gi|270015040|gb|EFA11488.1| hypothetical protein TcasGA2_TC014200 [Tribolium castaneum] Back     alignment and taxonomy information
>gi|189233719|ref|XP_969907.2| PREDICTED: similar to HGTX CG13475-PA [Tribolium castaneum] Back     alignment and taxonomy information
>gi|21358053|ref|NP_652614.1| HGTX [Drosophila melanogaster] gi|6969438|gb|AAF33780.1|AF220236_1 GTX/Nkx6B-like homeodomain protein [Drosophila melanogaster] gi|23093480|gb|AAF49729.3| HGTX [Drosophila melanogaster] gi|54650596|gb|AAV36877.1| RE53769p [Drosophila melanogaster] gi|66571254|gb|AAY51592.1| IP01125p [Drosophila melanogaster] gi|220943318|gb|ACL84202.1| HGTX-PA [synthetic construct] gi|220943456|gb|ACL84271.1| HGTX-PA [synthetic construct] gi|220953300|gb|ACL89193.1| HGTX-PA [synthetic construct] Back     alignment and taxonomy information
>gi|19528431|gb|AAL90330.1| RE18506p [Drosophila melanogaster] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query76
UNIPROTKB|E1BNQ7366 NKX6-1 "Uncharacterized protei 0.684 0.142 0.923 1.9e-21
UNIPROTKB|E2RRG1288 NKX6-1 "Uncharacterized protei 0.684 0.180 0.923 1.9e-21
UNIPROTKB|P78426367 NKX6-1 "Homeobox protein Nkx-6 0.684 0.141 0.923 1.9e-21
UNIPROTKB|F1RW12283 NKX6-1 "Uncharacterized protei 0.684 0.183 0.923 1.9e-21
UNIPROTKB|Q60554364 NKX6-1 "Homeobox protein Nkx-6 0.684 0.142 0.923 1.9e-21
MGI|MGI:1206039365 Nkx6-1 "NK6 homeobox 1" [Mus m 0.684 0.142 0.923 1.9e-21
RGD|69318365 Nkx6-1 "NK6 homeobox 1" [Rattu 0.684 0.142 0.923 1.9e-21
ZFIN|ZDB-GENE-040718-178312 nkx6.1 "NK6 transcription fact 0.684 0.166 0.923 1.9e-21
UNIPROTKB|F1NNJ9278 NKX6-2 "Uncharacterized protei 0.684 0.187 0.923 2.4e-21
UNIPROTKB|F1NYF2133 NKX6-2 "Uncharacterized protei 0.684 0.390 0.923 2.4e-21
UNIPROTKB|E1BNQ7 NKX6-1 "Uncharacterized protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 48/52 (92%), Positives = 51/52 (98%)

Query:     4 DKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
             DKD K+KHTRPTFSGQQIFALEKTFEQTKYLAGPERA+LAY+LGMTESQVKV
Sbjct:   229 DKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAYSLGMTESQVKV 280
GO:0005634 "nucleus" evidence=IEA
GO:0048709 "oligodendrocyte differentiation" evidence=IEA
GO:0045687 "positive regulation of glial cell differentiation" evidence=IEA
GO:0045686 "negative regulation of glial cell differentiation" evidence=IEA
GO:0045666 "positive regulation of neuron differentiation" evidence=IEA
GO:0031018 "endocrine pancreas development" evidence=IEA
GO:0021913 "regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification" evidence=IEA
GO:0021912 "regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification" evidence=IEA
GO:0007224 "smoothened signaling pathway" evidence=IEA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA
UNIPROTKB|E2RRG1 NKX6-1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|P78426 NKX6-1 "Homeobox protein Nkx-6.1" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RW12 NKX6-1 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q60554 NKX6-1 "Homeobox protein Nkx-6.1" [Mesocricetus auratus (taxid:10036)] Back     alignment and assigned GO terms
MGI|MGI:1206039 Nkx6-1 "NK6 homeobox 1" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|69318 Nkx6-1 "NK6 homeobox 1" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-040718-178 nkx6.1 "NK6 transcription factor related, locus 1 (Drosophila)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
UNIPROTKB|F1NNJ9 NKX6-2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|F1NYF2 NKX6-2 "Uncharacterized protein" [Gallus gallus (taxid:9031)] 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) ?
Q99MA9NKX61_MOUSENo assigned EC number0.92300.68420.1424yesN/A
Q9C056NKX62_HUMANNo assigned EC number0.92300.68420.1877noN/A
P78426NKX61_HUMANNo assigned EC number0.92300.68420.1416yesN/A
Q60554NKX61_MESAUNo assigned EC number0.92300.68420.1428N/AN/A
O35762NKX61_RATNo assigned EC number0.92300.68420.1424yesN/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 ?
Query76
pfam0004657 pfam00046, Homeobox, Homeobox domain 6e-13
smart0038957 smart00389, HOX, Homeodomain 5e-11
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 2e-10
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 56.7 bits (138), Expect = 6e-13
 Identities = 22/46 (47%), Positives = 31/46 (67%)

Query: 10 KHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
          +  R TF+ +Q+  LEK FE+ +Y +  ER +LA  LG+TE QVKV
Sbjct: 1  RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKV 46

Length = 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 76
KOG0489|consensus261 99.88
KOG0850|consensus245 99.87
KOG0488|consensus309 99.86
KOG0843|consensus197 99.84
KOG0484|consensus125 99.84
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.83
KOG0842|consensus307 99.82
KOG0487|consensus308 99.82
KOG0485|consensus268 99.8
KOG0848|consensus317 99.79
KOG0494|consensus 332 99.78
KOG0492|consensus246 99.78
KOG2251|consensus 228 99.78
COG5576156 Homeodomain-containing transcription factor [Trans 99.76
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.75
KOG0493|consensus342 99.75
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.73
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.73
KOG0491|consensus194 99.72
KOG0483|consensus198 99.66
KOG0486|consensus 351 99.65
KOG0844|consensus 408 99.6
KOG0847|consensus288 99.59
KOG4577|consensus 383 99.59
KOG3802|consensus398 99.58
KOG0490|consensus 235 99.48
KOG0849|consensus 354 99.4
KOG1168|consensus385 99.12
KOG0775|consensus304 99.04
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.94
KOG2252|consensus558 98.9
KOG0774|consensus334 98.87
KOG0490|consensus235 98.64
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 98.21
KOG1146|consensus 1406 98.12
KOG0773|consensus342 97.22
KOG3623|consensus 1007 97.2
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 96.55
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 94.99
COG3413215 Predicted DNA binding protein [General function pr 94.14
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 93.86
PF1066860 Phage_terminase: Phage terminase small subunit; In 93.02
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 92.59
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 91.94
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 91.91
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 90.52
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 90.4
PRK09413121 IS2 repressor TnpA; Reviewed 89.3
PF0605658 Terminase_5: Putative ATPase subunit of terminase 89.16
PRK09644165 RNA polymerase sigma factor SigM; Provisional 88.38
PRK03975141 tfx putative transcriptional regulator; Provisiona 88.1
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 88.09
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 87.88
PRK06759154 RNA polymerase factor sigma-70; Validated 87.66
PF1351852 HTH_28: Helix-turn-helix domain 87.51
PRK00118104 putative DNA-binding protein; Validated 87.22
PF0960758 BrkDBD: Brinker DNA-binding domain; InterPro: IPR0 86.94
PRK12526206 RNA polymerase sigma factor; Provisional 86.88
PRK12514179 RNA polymerase sigma factor; Provisional 86.59
PRK12512184 RNA polymerase sigma factor; Provisional 86.46
PRK11924179 RNA polymerase sigma factor; Provisional 86.43
PF1338450 HTH_23: Homeodomain-like domain; PDB: 2X48_C. 86.24
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 86.19
cd0476149 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of 86.12
TIGR0387973 near_KaiC_dom probable regulatory domain. This mod 85.88
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 85.86
PRK04217110 hypothetical protein; Provisional 85.72
PRK05602186 RNA polymerase sigma factor; Reviewed 85.66
PF1341169 MerR_1: MerR HTH family regulatory protein; PDB: 2 85.44
TIGR02939190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 85.41
PRK12546188 RNA polymerase sigma factor; Provisional 84.97
PRK12519194 RNA polymerase sigma factor; Provisional 84.83
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 84.66
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 84.36
PRK12524196 RNA polymerase sigma factor; Provisional 84.32
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 84.28
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family. Thi 83.88
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 83.85
PRK12537182 RNA polymerase sigma factor; Provisional 83.69
PRK09639166 RNA polymerase sigma factor SigX; Provisional 83.65
PRK12530189 RNA polymerase sigma factor; Provisional 83.62
PRK1007296 putative transcriptional regulator; Provisional 83.58
PRK09648189 RNA polymerase sigma factor SigD; Reviewed 83.56
PF0037638 MerR: MerR family regulatory protein; InterPro: IP 83.43
TIGR02948187 SigW_bacill RNA polymerase sigma-W factor. This si 83.42
PRK12541161 RNA polymerase sigma factor; Provisional 83.2
PRK12547164 RNA polymerase sigma factor; Provisional 82.94
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 82.9
PF0828059 HTH_Mga: M protein trans-acting positive regulator 82.5
PRK09047161 RNA polymerase factor sigma-70; Validated 82.37
TIGR02954169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 81.32
PRK12536181 RNA polymerase sigma factor; Provisional 80.98
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 80.82
PRK09645173 RNA polymerase sigma factor SigL; Provisional 80.7
cd0476467 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom 80.67
cd0476368 HTH_MlrA-like Helix-Turn-Helix DNA binding domain 80.46
PRK12515189 RNA polymerase sigma factor; Provisional 80.46
PRK13919186 putative RNA polymerase sigma E protein; Provision 80.39
PRK12538233 RNA polymerase sigma factor; Provisional 80.31
>KOG0489|consensus Back     alignment and domain information 
Probab=99.88  E-value=5.7e-23  Score=126.08  Aligned_cols=67  Identities=34%  Similarity=0.431  Sum_probs=62.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCcc
Q psy5355           6 DAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTES   72 (76)
Q Consensus         6 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~~   72 (76)
                      .+..+|.||.||..|+.+||..|..|.|++...|.+||..|.|+++||+|||| |||||||..+....
T Consensus       156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~  223 (261)
T KOG0489|consen  156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS  223 (261)
T ss_pred             cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence            45679999999999999999999999999999999999999999999999999 99999998766543

>KOG0850|consensus Back     alignment and domain information
>KOG0488|consensus Back     alignment and domain information
>KOG0843|consensus Back     alignment and domain information
>KOG0484|consensus Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0842|consensus Back     alignment and domain information
>KOG0487|consensus Back     alignment and domain information
>KOG0485|consensus Back     alignment and domain information
>KOG0848|consensus Back     alignment and domain information
>KOG0494|consensus Back     alignment and domain information
>KOG0492|consensus Back     alignment and domain information
>KOG2251|consensus Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0493|consensus Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>KOG0491|consensus Back     alignment and domain information
>KOG0483|consensus Back     alignment and domain information
>KOG0486|consensus Back     alignment and domain information
>KOG0844|consensus Back     alignment and domain information
>KOG0847|consensus Back     alignment and domain information
>KOG4577|consensus Back     alignment and domain information
>KOG3802|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>KOG0849|consensus Back     alignment and domain information
>KOG1168|consensus Back     alignment and domain information
>KOG0775|consensus Back     alignment and domain information
>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
>KOG2252|consensus Back     alignment and domain information
>KOG0774|consensus Back     alignment and domain information
>KOG0490|consensus Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>KOG1146|consensus Back     alignment and domain information
>KOG0773|consensus Back     alignment and domain information
>KOG3623|consensus Back     alignment and domain information
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere Back     alignment and domain information
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>COG3413 Predicted DNA binding protein [General function prediction only] 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
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes Back     alignment and domain information
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs) Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed Back     alignment and domain information
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after [] Back     alignment and domain information
>PRK09644 RNA polymerase sigma factor SigM; Provisional Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PF13518 HTH_28: Helix-turn-helix domain Back     alignment and domain information
>PRK00118 putative DNA-binding protein; Validated Back     alignment and domain information
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx Back     alignment and domain information
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12512 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily Back     alignment and domain information
>TIGR03879 near_KaiC_dom probable regulatory domain Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>PRK04217 hypothetical protein; Provisional Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK12546 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK10072 putative transcriptional regulator; Provisional Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities Back     alignment and domain information
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12547 RNA polymerase sigma factor; Provisional 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
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [] Back     alignment and domain information
>PRK09047 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators Back     alignment and domain information
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional 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 ?
Query76
2djn_A70 The Solution Structure Of The Homeobox Domain Of Hu 6e-07
3rkq_A58 Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Lengt 2e-06
1ftt_A68 Thyroid Transcription Factor 1 Homeodomain (Rattus 4e-06
2dmt_A80 Solution Structure Of The Homeobox Domain Of Homeob 6e-06
3a01_A93 Crystal Structure Of Aristaless And Clawless Homeod 6e-06
3a03_A56 Crystal Structure Of Hox11l1 Homeodomain Length = 5 7e-06
2m34_A71 Nmr Structure Of The Homeodomain Transcription Fact 1e-05
2l9r_A69 Solution Nmr Structure Of Homeobox Domain Of Homeob 3e-05
1nk2_P77 VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES 3e-05
2e1o_A70 Solution Structure Of Rsgi Ruh-028, A Homeobox Doma 3e-05
1ig7_A58 Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 4e-05
2h1k_A63 Crystal Structure Of The Pdx1 Homeodomain In Comple 9e-05
1qry_A80 Homeobox Protein Vnd (Ventral Nervous System Defect 1e-04
9ant_A62 Antennapedia Homeodomain-Dna Complex Length = 62 2e-04
1p7j_A59 Crystal Structure Of Engrailed Homeodomain Mutant K 2e-04
1ahd_P68 Determination Of The Nmr Solution Structure Of An A 4e-04
1hom_A68 Determination Of The Three-Dimensional Structure Of 5e-04
1hdd_C61 Crystal Structure Of An Engrailed Homeodomain-Dna C 6e-04
1zq3_P68 Nmr Solution Structure Of The Bicoid Homeodomain Bo 7e-04
2hdd_A61 Engrailed Homeodomain Q50k Variant Dna Complex Leng 7e-04
1b8i_A81 Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX 7e-04
1p7i_A59 Crystal Structure Of Engrailed Homeodomain Mutant K 8e-04
3hdd_A60 Engrailed Homeodomain Dna Complex Length = 60 8e-04
1ftz_A70 Nuclear Magnetic Resonance Solution Structure Of Th 8e-04
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5 Length = 70 Back     alignment and structure 
Iteration: 1

 Score = 49.3 bits (116), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 22/43 (51%), Positives = 35/43 (81%)
Query: 13 RPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
          R  +S  Q+ AL++ F++T+YLA PERA+LA +LG+T++QVK+
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKI 53
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna Length = 58 Back     alignment and structure
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus Norvegicus) Length = 68 Back     alignment and structure
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Barh-Like 1 Length = 80 Back     alignment and structure
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains Bo Length = 93 Back     alignment and structure
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain Length = 56 Back     alignment and structure
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1 From Homo Sapiens Length = 71 Back     alignment and structure
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox Protein Nkx-3.1 From Homo Sapiens, Northeast Structural Genomics Consortium Target Hr6470a Length = 69 Back     alignment and structure
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES Length = 77 Back     alignment and structure
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna Length = 70 Back     alignment and structure
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE Length = 58 Back     alignment and structure
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With Dna Length = 63 Back     alignment and structure
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective Protein) Length = 80 Back     alignment and structure
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex Length = 62 Back     alignment and structure
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e Length = 59 Back     alignment and structure
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An Antennapedia Homeodomain-Dna Complex Length = 68 Back     alignment and structure
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The Antennapedia Homeodomain From Drosophila In Solution By 1h Nuclear Magnetic Resonance Spectroscopy Length = 68 Back     alignment and structure
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61 Back     alignment and structure
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To The Consensus Dna Binding Site Taatcc Length = 68 Back     alignment and structure
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex Length = 61 Back     alignment and structure
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 81 Back     alignment and structure
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a Length = 59 Back     alignment and structure
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60 Back     alignment and structure
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi Tarazu Homeodomain From Drosophila And Comparison With The Antennapedia Homeodomain Length = 70 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query76
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 3e-16
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 5e-16
3a01_A93 Homeodomain-containing protein; homeodomain, prote 7e-16
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 8e-16
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 1e-15
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 3e-15
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 4e-15
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 6e-15
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 1e-14
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 1e-14
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 3e-14
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 1e-13
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 1e-13
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 6e-11
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 5e-10
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 1e-09
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 1e-09
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 2e-09
1e3o_C160 Octamer-binding transcription factor 1; transcript 3e-09
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 3e-09
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 6e-09
2xsd_C164 POU domain, class 3, transcription factor 1; trans 7e-09
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 9e-09
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 1e-08
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 3e-08
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 5e-08
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 6e-08
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 9e-08
3d1n_I151 POU domain, class 6, transcription factor 1; prote 2e-07
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 2e-07
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 3e-07
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 4e-07
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 5e-07
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 5e-07
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 7e-07
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 1e-06
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 1e-06
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 1e-06
3a02_A60 Homeobox protein aristaless; homeodomain, developm 2e-06
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 3e-06
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 3e-06
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 3e-06
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 4e-06
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 5e-06
1uhs_A72 HOP, homeodomain only protein; structural genomics 6e-06
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 9e-06
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 1e-05
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 2e-05
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 2e-05
1lfb_A99 Liver transcription factor (LFB1); transcription r 6e-05
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 2e-04
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 3e-04
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 6e-04
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69 Back     alignment and structure
 Score = 65.1 bits (159), Expect = 3e-16
 Identities = 21/49 (42%), Positives = 27/49 (55%)

Query: 7  AKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
              H     S  Q+  LE+ F   KYL+ PERA LA  L +TE+QVK+
Sbjct: 2  GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKI 50
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93 Back     alignment and structure
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77 Back     alignment and structure
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62 Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58 Back     alignment and structure
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84 Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56 Back     alignment and structure
>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
>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
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68 Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61 Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60 Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Length = 63 Back     alignment and structure
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 Length = 97 Back     alignment and structure
>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
>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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Length = 88 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
>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
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Length = 81 Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Length = 68 Back     alignment and structure
>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
>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
>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
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A Length = 77 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 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
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80 Back     alignment and structure
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70 Back     alignment and structure
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Length = 73 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
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60 Back     alignment and structure
>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
>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
>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
>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
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 Back     alignment and structure
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 95 Back     alignment and structure
>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
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99 Back     alignment and structure
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query76
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.91
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.91
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.91
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.91
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.91
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.91
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.91
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.91
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.91
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.91
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.91
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.91
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.9
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.9
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.9
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.9
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.9
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.9
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.9
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.9
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.9
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.9
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.9
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.9
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.9
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.89
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.89
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.89
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.89
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.89
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.89
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.89
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.89
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.89
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.89
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.88
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.88
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.88
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.88
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.88
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.88
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.88
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.88
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.88
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.88
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.87
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.87
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.87
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.86
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.85
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.85
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.85
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.85
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.85
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.85
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.85
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.85
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.84
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.84
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.84
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.84
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.84
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.84
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.84
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.83
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.83
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.83
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.83
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.81
2e19_A64 Transcription factor 8; homeobox domain, structura 99.8
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.8
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.76
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.69
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.66
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.64
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.63
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.54
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.72
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 97.66
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 93.89
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 92.64
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 92.19
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 91.98
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 91.15
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 91.12
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 91.12
1s7o_A113 Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP 88.9
3mzy_A164 RNA polymerase sigma-H factor; PSI, MCSG, structur 88.54
1xsv_A113 Hypothetical UPF0122 protein SAV1236; helix-turn-h 86.57
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 86.24
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 86.15
2rgt_A169 Fusion of LIM/homeobox protein LHX3, linker, INSU 85.52
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 85.12
1ku3_A73 Sigma factor SIGA; helix-turn-helix, transcription 84.28
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 84.1
1tty_A87 Sigma-A, RNA polymerase sigma factor RPOD; helix-t 83.93
1rp3_A239 RNA polymerase sigma factor sigma-28 (FLIA); trans 83.82
1iuf_A144 Centromere ABP1 protein; riken structural genomics 83.35
1u78_A141 TC3 transposase, transposable element TC3 transpos 83.25
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 81.53
>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
Probab=99.91  E-value=3e-24  Score=108.38  Aligned_cols=64  Identities=30%  Similarity=0.342  Sum_probs=59.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcC
Q psy5355           5 KDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALG   68 (76)
Q Consensus         5 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~   68 (76)
                      .++..++.|+.|+..|+..|+..|..++||+..++..||..|||++.+|+|||| +|+++++...
T Consensus         3 ~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             STTSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            445678899999999999999999999999999999999999999999999999 9999998654
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>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
>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
>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
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_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
>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
>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
>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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_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
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} 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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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
>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
>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
>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
>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
>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
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens} Back     alignment and structure
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_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
>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
>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
>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
>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
>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
>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
>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
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Back     alignment and structure
>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis} 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
>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
>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis} Back     alignment and structure
>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19 Back     alignment and structure
>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3 Back     alignment and structure
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Back     alignment and structure
>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3 Back     alignment and structure
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_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
>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
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Back     alignment and structure
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Back     alignment and structure
>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Back     alignment and structure
>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7 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
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 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 76
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 1e-11
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 5e-11
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 6e-11
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 7e-11
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 7e-11
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 1e-10
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 8e-10
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 1e-09
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 1e-09
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 3e-09
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 5e-09
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 8e-09
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 9e-09
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 2e-08
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 4e-08
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 5e-08
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 8e-08
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 1e-07
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 2e-07
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 2e-07
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 4e-07
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 6e-07
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 7e-07
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 9e-07
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 1e-06
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 1e-06
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 2e-06
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 3e-06
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 9e-06
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 5e-05
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 2e-04
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.1 bits (125), Expect = 1e-11
 Identities = 17/54 (31%), Positives = 24/54 (44%)

Query: 2  NSDKDAKKKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKV 55
          N       +  R  ++  Q   LEK F    YL    R ++A  L +TE QVK+
Sbjct: 6  NWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKI 59
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>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
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 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
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53 Back     information, alignment and structure
>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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58 Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 Back     information, alignment and structure
>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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67 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
>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
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 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
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80 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
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query76
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.93
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.93
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.93
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.93
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.93
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.92
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.92
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.92
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.92
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.92
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.91
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.91
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.91
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.91
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.91
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.89
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.89
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.89
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.88
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.88
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.88
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.87
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.86
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.85
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.84
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.83
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.83
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.8
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.8
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.77
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.77
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.76
d1hlva166 DNA-binding domain of centromere binding protein B 95.85
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 94.85
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 92.75
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 92.03
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 90.26
d1j9ia_68 Terminase gpNU1 subunit domain {Bacteriophage lamb 87.68
d1fsea_67 Germination protein GerE {Bacillus subtilis [TaxId 85.17
d2ppxa162 Uncharacterized protein Atu1735 {Agrobacterium tum 81.58
d1bl0a154 MarA {Escherichia coli [TaxId: 562]} 81.37
d2pq3a173 Calmodulin {Rattus norvegicus [TaxId: 10116]} 81.06
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.93  E-value=4.1e-26  Score=113.10  Aligned_cols=63  Identities=32%  Similarity=0.422  Sum_probs=58.2

Q ss_pred             CCCCCCCCCHHHHHHHHHhccccCCCCHHHHHHHHHHhCCCchhHHHhhH-hHHHHHHHcCCCc
Q psy5355           9 KKHTRPTFSGQQIFALEKTFEQTKYLAGPERAKLAYALGMTESQVKVTGP-ERAKLAYALGMTE   71 (76)
Q Consensus         9 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~La~~l~l~~~qV~vWFq-rR~k~kk~~~~~~   71 (76)
                      +++.|+.||+.|+.+|+..|..++||+..++..||..|||++.+|+|||| +|+++++.....+
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~~   64 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHK   64 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhcc
Confidence            46789999999999999999999999999999999999999999999999 9999998765443
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>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
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} 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
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]} Back     information, alignment and structure
>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Back     information, alignment and structure
>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2pq3a1 a.39.1.5 (A:3-75) Calmodulin {Rattus norvegicus [TaxId: 10116]} Back     information, alignment and structure