Citrus Sinensis ID: 047211

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280--
FSCKNIFHFSLSTVMEDQSQDANNNSPSRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAGEQRNNNIQQAQASSAAGAIQYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSRPA
ccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccEEEEcccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHHHHccccEEEEcccccccccccccccccccccccEEEEEEccc
ccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccHHHHHHcHHHHHHHHHHHHHHcccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccEcccEEEEEEEccccEEcccccccHHHHHcccEEEEEccccccccccccEEEEccccccEEEEEEccc
fscknifhfsLSTVmedqsqdannnspsrgsaerstepvrsrwtpkpeQILILESIFnsgmvnppkdETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAGEQRNNNIQQAQASSAAGAIQYEINSNCAaaalpmgfaatspatfgstpctnfvagsssfcgvmggddgvETLYSVSGqmgfqevvdqnssvtsmlcpsessnlqyqTGFITVFIngapteiprgpidmkalfgQDVVLVhssgvpiptnefGFLMQSLQHGESYFLVSRPA
FSCKNIFHFSLStvmedqsqdannnspsrgsaerstepvrsrwtpkpEQILILEsifnsgmvnppKDETVRIRKLLEkfgsvgdanvfywfqnrrsrsrRRQRQLQAslageqrnnnIQQAQASSAAGAIQYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSRPA
FSCKNIFHFSLSTVMEDQSQDANNNSPSRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNrrsrsrrrqrqlqaslaGEqrnnniqqaqassaagaiqYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSRPA
******F*****************************************QILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQ************************************AIQYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVD*******MLC*****NLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFL*****
********************************************PKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWF*********************************************************************************************************************************ITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR**
FSCKNIFHFSLSTVME***************************TPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNR**************LAGEQRNNN**********GAIQYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSRPA
****************************************SRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR********************************************************************************VETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSR**
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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FSCKNIFHFSLSTVMEDQSQDANNNSPSRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAGEQRNNNIQQAQASSAAGAIQYEINSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSFCGVMGGDDGVETLYSVSGQMGFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPIPTNEFGFLMQSLQHGESYFLVSRPA
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 ?
Query282 2.2.26 [Sep-21-2011]
Q6X7J3268 WUSCHEL-related homeobox yes no 0.847 0.891 0.579 2e-65
Q8GY25268 WUSCHEL-related homeobox no no 0.882 0.929 0.510 2e-59
Q0D3I7262 WUSCHEL-related homeobox yes no 0.897 0.965 0.505 8e-52
Q6Z3L4284 WUSCHEL-related homeobox no no 0.861 0.855 0.475 2e-44
A2YST1284 WUSCHEL-related homeobox N/A no 0.936 0.929 0.449 3e-44
Q6X7J5325 WUSCHEL-related homeobox no no 0.971 0.843 0.334 1e-32
A2XG77328 WUSCHEL-related homeobox N/A no 0.202 0.173 0.964 7e-28
Q6X7J4378 WUSCHEL-related homeobox no no 0.262 0.195 0.666 3e-24
Q0JKK6 533 WUSCHEL-related homeobox no no 0.343 0.181 0.540 2e-23
A3B6V0 515 WUSCHEL-related homeobox no no 0.237 0.130 0.661 2e-22
>sp|Q6X7J3|WOX11_ARATH WUSCHEL-related homeobox 11 OS=Arabidopsis thaliana GN=WOX11 PE=2 SV=2 Back     alignment and function desciption
 Score =  249 bits (635), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 153/264 (57%), Positives = 186/264 (70%), Gaps = 25/264 (9%)

Query: 27  PSRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDAN 86
           PS  S   S EPVRSRW+PKPEQILILESIF+SGMVNPPK+ETVRIRK+LEKFG+VGDAN
Sbjct: 18  PSSASGSTSAEPVRSRWSPKPEQILILESIFHSGMVNPPKEETVRIRKMLEKFGAVGDAN 77

Query: 87  VFYWFQNRRSRSRRRQRQLQASLAGEQRNNNIQQAQASSAAGAIQYEINSNCAAAALPMG 146
           VFYWFQNRRSRSRRRQRQLQA+ A      N    Q    + ++ +   S+       +G
Sbjct: 78  VFYWFQNRRSRSRRRQRQLQAAAAAADATTNTCD-QTMMVSNSLPHHSGSD-------LG 129

Query: 147 FAATSPATFGSTPCTNFVAGSSSFCGVMGGDD----GVETLYSVSGQMGFQEVV-----D 197
           F        G +  +N++  SSS     G D+    G+E L ++SGQM + E       +
Sbjct: 130 FG-------GCSTSSNYLFASSSSSYGGGCDNQSNSGMENLLTMSGQMSYHEATHHHYQN 182

Query: 198 QNSSVTSMLCPSE-SSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVP 256
            +S+VTS+LCPS+ +SN QYQ G ITVFING PTE+ RG IDMKA FG+D+VLVHSSGVP
Sbjct: 183 HSSNVTSILCPSDQNSNFQYQQGAITVFINGVPTEVTRGGIDMKATFGEDLVLVHSSGVP 242

Query: 257 IPTNEFGFLMQSLQHGESYFLVSR 280
           +PT+EFGFLM SLQHGE+YFLV R
Sbjct: 243 LPTDEFGFLMHSLQHGEAYFLVPR 266
Transcription factor which may be involved in developmental processes.
Arabidopsis thaliana (taxid: 3702)
>sp|Q8GY25|WOX12_ARATH WUSCHEL-related homeobox 12 OS=Arabidopsis thaliana GN=WOX12 PE=2 SV=1 Back     alignment and function description
>sp|Q0D3I7|WOX11_ORYSJ WUSCHEL-related homeobox 11 OS=Oryza sativa subsp. japonica GN=WOX11 PE=2 SV=1 Back     alignment and function description
>sp|Q6Z3L4|WOX10_ORYSJ WUSCHEL-related homeobox 10 OS=Oryza sativa subsp. japonica GN=WOX10 PE=2 SV=1 Back     alignment and function description
>sp|A2YST1|WOX10_ORYSI WUSCHEL-related homeobox 10 OS=Oryza sativa subsp. indica GN=WOX10 PE=2 SV=1 Back     alignment and function description
>sp|Q6X7J5|WOX8_ARATH WUSCHEL-related homeobox 8 OS=Arabidopsis thaliana GN=WOX8 PE=2 SV=1 Back     alignment and function description
>sp|A2XG77|WOX6_ORYSI WUSCHEL-related homeobox 6 OS=Oryza sativa subsp. indica GN=WOX6 PE=2 SV=1 Back     alignment and function description
>sp|Q6X7J4|WOX9_ARATH WUSCHEL-related homeobox 9 OS=Arabidopsis thaliana GN=WOX9 PE=2 SV=1 Back     alignment and function description
>sp|Q0JKK6|WOX7_ORYSJ WUSCHEL-related homeobox 7 OS=Oryza sativa subsp. japonica GN=WOX7 PE=2 SV=2 Back     alignment and function description
>sp|A3B6V0|WOX12_ORYSJ WUSCHEL-related homeobox 12 OS=Oryza sativa subsp. japonica GN=WOX12 PE=2 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 ?
Query282
255569408261 Protein WUSCHEL, putative [Ricinus commu 0.897 0.969 0.702 3e-87
224123922255 predicted protein [Populus trichocarpa] 0.875 0.968 0.737 3e-84
224144863226 predicted protein [Populus trichocarpa] 0.794 0.991 0.631 6e-75
359481008236 PREDICTED: WUSCHEL-related homeobox 11-l 0.826 0.987 0.641 5e-73
357508903272 WUSCHEL-related homeobox [Medicago trunc 0.907 0.941 0.570 4e-64
145338074268 WUSCHEL related homeobox 11 [Arabidopsis 0.847 0.891 0.579 1e-63
297811943266 predicted protein [Arabidopsis lyrata su 0.897 0.951 0.540 2e-63
388510020272 unknown [Medicago truncatula] 0.907 0.941 0.567 2e-63
37955223268 WOX11 protein [Arabidopsis thaliana] 0.847 0.891 0.575 3e-63
124360469325 Homeodomain-related [Medicago truncatula 0.897 0.778 0.569 2e-62
>gi|255569408|ref|XP_002525671.1| Protein WUSCHEL, putative [Ricinus communis] gi|223534971|gb|EEF36654.1| Protein WUSCHEL, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  327 bits (839), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 189/269 (70%), Positives = 214/269 (79%), Gaps = 16/269 (5%)

Query: 15  MEDQSQDANNNSPSRGSAERSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRK 74
           MED     +NNSP     ERS EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRK
Sbjct: 1   MEDNQGQDSNNSPRNQGTERS-EPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRK 59

Query: 75  LLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQASLAGEQRNNNIQQAQASSAAGAIQYEI 134
           LLEKFGSVGDANVFYWFQNRRSRSRRRQRQ+QA+LA EQRN   QQAQAS   GAIQY+ 
Sbjct: 60  LLEKFGSVGDANVFYWFQNRRSRSRRRQRQMQATLAEEQRN---QQAQAS--GGAIQYDG 114

Query: 135 NSNCAAAALPMGFAATSPATFGSTPCTNFVAGSSSF-CGVM--GGDDGV-ETLYSVSGQM 190
            S  +     +GFA +S  +  S     FV GSS+  CG++  GG+DGV   LYS+  QM
Sbjct: 115 GSTSS-----LGFANSSSFSAVSVSPPPFVVGSSTTSCGLVACGGEDGVANNLYSIPNQM 169

Query: 191 GFQEVVDQNSSVTSMLCPSESSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLV 250
           GFQE +   S ++S+LCP+E+SNL YQTGFITVFING PTE+PRGP+DMKA+FGQDVVLV
Sbjct: 170 GFQE-MGHTSGISSILCPTETSNLNYQTGFITVFINGVPTEVPRGPLDMKAMFGQDVVLV 228

Query: 251 HSSGVPIPTNEFGFLMQSLQHGESYFLVS 279
           HSSG+P+PTNEFGFLM SLQHGESYFLV+
Sbjct: 229 HSSGMPVPTNEFGFLMHSLQHGESYFLVN 257

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224123922|ref|XP_002319197.1| predicted protein [Populus trichocarpa] gi|224123926|ref|XP_002319198.1| predicted protein [Populus trichocarpa] gi|222857573|gb|EEE95120.1| predicted protein [Populus trichocarpa] gi|222857574|gb|EEE95121.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224144863|ref|XP_002325442.1| predicted protein [Populus trichocarpa] gi|222862317|gb|EEE99823.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359481008|ref|XP_002269282.2| PREDICTED: WUSCHEL-related homeobox 11-like [Vitis vinifera] gi|296085887|emb|CBI31211.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|357508903|ref|XP_003624740.1| WUSCHEL-related homeobox [Medicago truncatula] gi|217074296|gb|ACJ85508.1| unknown [Medicago truncatula] gi|355499755|gb|AES80958.1| WUSCHEL-related homeobox [Medicago truncatula] Back     alignment and taxonomy information
>gi|145338074|ref|NP_187016.2| WUSCHEL related homeobox 11 [Arabidopsis thaliana] gi|342187324|sp|Q6X7J3.2|WOX11_ARATH RecName: Full=WUSCHEL-related homeobox 11 gi|332640447|gb|AEE73968.1| WUSCHEL related homeobox 11 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297811943|ref|XP_002873855.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297319692|gb|EFH50114.1| predicted protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|388510020|gb|AFK43076.1| unknown [Medicago truncatula] Back     alignment and taxonomy information
>gi|37955223|gb|AAP37140.1| WOX11 protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|124360469|gb|ABN08479.1| Homeodomain-related [Medicago truncatula] 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 ?
Query282
TAIR|locus:2096429297 WOX11 "AT3G03660" [Arabidopsis 0.460 0.437 0.587 3.3e-65
TAIR|locus:2175941268 WOX12 "AT5G17810" [Arabidopsis 0.900 0.947 0.468 1.1e-55
TAIR|locus:2057614378 HB-3 "homeobox-3" [Arabidopsis 0.251 0.187 0.648 8.1e-36
TAIR|locus:2161353325 WOX8 "AT5G45980" [Arabidopsis 0.319 0.276 0.505 2.4e-33
TAIR|locus:2060902292 WUS "AT2G17950" [Arabidopsis t 0.269 0.260 0.410 3.3e-09
TAIR|locus:2166434122 WOX7 "AT5G05770" [Arabidopsis 0.234 0.540 0.352 5.6e-08
TAIR|locus:2074638182 WOX5 "WUSCHEL related homeobox 0.230 0.357 0.384 3.5e-07
TAIR|locus:2049547271 PFS2 "PRETTY FEW SEEDS 2" [Ara 0.184 0.191 0.461 4.5e-07
UNIPROTKB|Q33DK1203 WOX3 "WUSCHEL-related homeobox 0.187 0.261 0.452 4.9e-07
TAIR|locus:2088550350 WOX1 "WUSCHEL related homeobox 0.301 0.242 0.305 6.6e-07
TAIR|locus:2096429 WOX11 "AT3G03660" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 378 (138.1 bits), Expect = 3.3e-65, Sum P(2) = 3.3e-65
 Identities = 84/143 (58%), Positives = 104/143 (72%)

Query:   149 ATSPATFGSTPCTNFVAGSSSFCGVMGGDD-----GVETLYSVSGQMGFQEVVD---QN- 199
             ++SP++  S+  T+  A SSS  G  GG D     G+E L ++SGQM + E      QN 
Sbjct:   155 SSSPSSCSSSSSTSSSASSSSSYG--GGCDNQSNSGMENLLTMSGQMSYHEATHHHYQNH 212

Query:   200 -SSVTSMLCPSE-SSNLQYQTGFITVFINGAPTEIPRGPIDMKALFGQDVVLVHSSGVPI 257
              S+VTS+LCPS+ +SN QYQ G ITVFING PTE+ RG IDMKA FG+D+VLVHSSGVP+
Sbjct:   213 SSNVTSILCPSDQNSNFQYQQGAITVFINGVPTEVTRGGIDMKATFGEDLVLVHSSGVPL 272

Query:   258 PTNEFGFLMQSLQHGESYFLVSR 280
             PT+EFGFLM SLQHGE+YFLV R
Sbjct:   273 PTDEFGFLMHSLQHGEAYFLVPR 295
GO:0003677 "DNA binding" evidence=ISS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0016114 "terpenoid biosynthetic process" evidence=RCA
TAIR|locus:2175941 WOX12 "AT5G17810" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2057614 HB-3 "homeobox-3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2161353 WOX8 "AT5G45980" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2060902 WUS "AT2G17950" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2166434 WOX7 "AT5G05770" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2074638 WOX5 "WUSCHEL related homeobox 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2049547 PFS2 "PRETTY FEW SEEDS 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q33DK1 WOX3 "WUSCHEL-related homeobox 3" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2088550 WOX1 "WUSCHEL related homeobox 1" [Arabidopsis thaliana (taxid:3702)] 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) ?
Q6X7J3WOX11_ARATHNo assigned EC number0.57950.84750.8917yesno
Q0D3I7WOX11_ORYSJNo assigned EC number0.50570.89710.9656yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
eugene3.00130648
SubName- Full=WOX11/12A protein; Flags- Fragment; (255 aa)
(Populus trichocarpa)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query282
pfam0004657 pfam00046, Homeobox, Homeobox domain 3e-11
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 2e-07
smart0038957 smart00389, HOX, Homeodomain 4e-07
COG5576156 COG5576, COG5576, Homeodomain-containing transcrip 2e-04
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information 
 Score = 57.1 bits (139), Expect = 3e-11
 Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 40  RSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99
           R R T  PEQ+  LE  F      P  +E   + K L     + +  V  WFQNRR++ +
Sbjct: 2   RKRTTFTPEQLEELEKEFEKNR-YPSAEEREELAKKL----GLTERQVKVWFQNRRAKWK 56

Query: 100 R 100
           R
Sbjct: 57  R 57

Length = 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 282
KOG0489261 consensus Transcription factor zerknullt and relat 99.78
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.77
KOG0488309 consensus Transcription factor BarH and related HO 99.75
KOG0843197 consensus Transcription factor EMX1 and related HO 99.75
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.74
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.67
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.67
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.66
KOG0848317 consensus Transcription factor Caudal, contains HO 99.65
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.64
KOG0493342 consensus Transcription factor Engrailed, contains 99.6
KOG2251228 consensus Homeobox transcription factor [Transcrip 99.59
KOG0850245 consensus Transcription factor DLX and related pro 99.59
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.57
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.54
KOG0494332 consensus Transcription factor CHX10 and related H 99.54
COG5576156 Homeodomain-containing transcription factor [Trans 99.53
KOG0483198 consensus Transcription factor HEX, contains HOX a 99.51
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.5
KOG0844408 consensus Transcription factor EVX1, contains HOX 99.49
KOG4577383 consensus Transcription factor LIM3, contains LIM 99.48
KOG3802398 consensus Transcription factor OCT-1, contains POU 99.41
KOG0491194 consensus Transcription factor BSH, contains HOX d 99.4
KOG0486351 consensus Transcription factor PTX1, contains HOX 99.4
KOG0490235 consensus Transcription factor, contains HOX domai 99.28
KOG0847288 consensus Transcription factor, contains HOX domai 99.25
KOG0849354 consensus Transcription factor PRD and related pro 99.06
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 98.92
KOG2252558 consensus CCAAT displacement protein and related h 98.2
KOG0775304 consensus Transcription factor SIX and related HOX 98.2
KOG0490235 consensus Transcription factor, contains HOX domai 98.19
KOG0774334 consensus Transcription factor PBX and related HOX 97.66
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 97.46
KOG1146 1406 consensus Homeobox protein [General function predi 97.15
KOG0773342 consensus Transcription factor MEIS1 and related H 95.7
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 95.12
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 90.45
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 90.44
PRK0805366 sulfur carrier protein ThiS; Provisional 85.48
PRK0769667 sulfur carrier protein ThiS; Provisional 80.42
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only] Back     alignment and domain information 
Probab=99.78  E-value=2.4e-20  Score=171.15  Aligned_cols=68  Identities=22%  Similarity=0.350  Sum_probs=61.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211           36 TEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS  108 (282)
Q Consensus        36 ~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~  108 (282)
                      +..||.|+.||..||.+||++|..|+ |..+.+|.+||..|    .|+|+||||||||||+||||+.+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~-YLtR~RRiEiA~~L----~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNK-YLTRSRRIEIAHAL----NLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhcccc-ccchHHHHHHHhhc----chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            34689999999999999999999999 59999999888888    7999999999999999999988776543

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>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
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription] Back     alignment and domain information
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>PRK08053 sulfur carrier protein ThiS; Provisional Back     alignment and domain information
>PRK07696 sulfur carrier protein ThiS; Provisional Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query282
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 1e-09
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 1e-06
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 2e-06
1lfb_A99 Liver transcription factor (LFB1); transcription r 3e-06
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 4e-06
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 6e-06
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 1e-05
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 2e-05
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 3e-05
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 4e-05
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 5e-05
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 7e-05
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 8e-05
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 9e-05
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 9e-05
1uhs_A72 HOP, homeodomain only protein; structural genomics 2e-04
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 3e-04
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 4e-04
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 5e-04
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 5e-04
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 6e-04
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 9e-04
>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
 Score = 53.5 bits (128), Expect = 1e-09
 Identities = 23/84 (27%), Positives = 33/84 (39%), Gaps = 12/84 (14%)

Query: 30  GSAERSTEPVRSRWTPKPEQILILESIFNSG----------MVNPPKDETVRIRKLLEKF 79
           GS+  S     SR+T + E + ++ES FN            + N       +  K L   
Sbjct: 1   GSSGSSGR--GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDL 58

Query: 80  GSVGDANVFYWFQNRRSRSRRRQR 103
             V    V+ WF NRR   +RR  
Sbjct: 59  ERVTSLKVYNWFANRRKEIKRRAN 82
>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
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Length = 194 Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Length = 99 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73 Back     alignment and structure
>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
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80 Back     alignment and structure
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 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
>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
>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
>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
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query282
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.83
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.82
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.82
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.82
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.81
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.81
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.81
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.81
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.81
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.81
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.81
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.8
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.8
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.8
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.8
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.8
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.8
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.8
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.79
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.79
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.79
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.79
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.79
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.79
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.78
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.78
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.78
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.78
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.78
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.78
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.78
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.78
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.77
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.77
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.77
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.77
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.77
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.77
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.76
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.76
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.76
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.76
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.75
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.75
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.75
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.74
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.74
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.74
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.73
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.73
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.72
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.72
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.72
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.72
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.71
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.71
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.7
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.7
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.69
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.69
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.69
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.69
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.68
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.68
2e19_A64 Transcription factor 8; homeobox domain, structura 99.67
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.67
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.66
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.65
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.64
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.64
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.61
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.54
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.51
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.41
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.38
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.34
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.29
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.84
1tyg_B87 YJBS; alpha beta barrel, protein-protein complex, 81.5
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 81.04
>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
Probab=99.83  E-value=2.8e-21  Score=146.41  Aligned_cols=70  Identities=26%  Similarity=0.363  Sum_probs=61.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHHHHHh
Q 047211           34 RSTEPVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQLQAS  108 (282)
Q Consensus        34 ~~~~~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~~q~~  108 (282)
                      ..+.++|+|+.||++|+.+||.+|..++ ||+..+|.+||.+|    +|++++|++||||||+|+|++++..++.
T Consensus         3 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~-yp~~~~r~~LA~~l----~l~~~qV~vWFqNRR~k~kk~~~~~~~~   72 (80)
T 2cue_A            3 SGSSGQRNRTSFTQEQIEALEKEFERTH-YPDVFARERLAAKI----DLPEARIQVWFSNRRAKWRREEKLRNQR   72 (80)
T ss_dssp             SCCSSCCCCCCSCHHHHHHHHHHHTTCS-SCCHHHHHHHHHHT----TCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCccCHHHHHHHHHHHhccC-CCCHHHHHHHHHHh----CCCHHHhhHHHHHHHHHHHHHhhhhhcc
Confidence            3456788999999999999999999998 59999887666666    8999999999999999999998776543
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Back     alignment and structure
>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
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Back     alignment and structure
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A* Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* 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
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>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
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 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
>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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2 Back     alignment and structure
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure

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 282
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 8e-10
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 5e-09
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 6e-09
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 3e-08
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 8e-08
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 2e-07
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 2e-07
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 3e-07
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 3e-07
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 6e-07
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 8e-07
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 1e-06
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 2e-06
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 3e-06
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 3e-06
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 6e-06
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 6e-06
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 9e-06
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 1e-05
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 2e-05
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 4e-05
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 5e-05
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 1e-04
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 2e-04
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 3e-04
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 4e-04
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 8e-04
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 9e-04
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 0.001
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 51.8 bits (124), Expect = 8e-10
 Identities = 10/67 (14%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 40  RSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSR 99
           R R     +Q+  L + + +        +   +         +    +  WFQN+R + +
Sbjct: 5   RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMT-----GLSPRVIRVWFQNKRCKDK 59

Query: 100 RRQRQLQ 106
           +R   ++
Sbjct: 60  KRSIMMK 66
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67 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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 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
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 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
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71 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
>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
>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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67 Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53 Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 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 ?
Query282
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.84
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.84
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.83
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.83
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.83
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.83
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.83
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.82
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.82
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.82
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.81
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.81
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.8
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.8
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.8
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.79
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.79
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.77
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.75
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.75
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.75
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.72
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.72
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.71
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.7
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.67
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.66
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.65
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.61
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.56
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.54
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.51
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 81.91
>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=99.84  E-value=2e-22  Score=148.85  Aligned_cols=62  Identities=34%  Similarity=0.457  Sum_probs=56.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhcCCCCCCceeecccccchhhHHHHHH
Q 047211           38 PVRSRWTPKPEQILILESIFNSGMVNPPKDETVRIRKLLEKFGSVGDANVFYWFQNRRSRSRRRQRQ  104 (282)
Q Consensus        38 ~kR~Rt~fT~eQL~~LE~~F~~~~~yP~~~eR~~Ia~eLa~~~~Lse~qVkvWFQNRRAK~KRk~r~  104 (282)
                      |+|+|+.||++|+.+||.+|+.++ ||+.++|.+||+.|    ||++++|+|||||||+|+|+...+
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~-yp~~~~r~~LA~~l----~l~~~~V~iWFqNrR~k~kk~~~~   62 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGR-YLTAPRLADLSAKL----ALGTAQVKIWFKNRRRRHKIQSDQ   62 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCS-SCCHHHHHHHHHHH----TSCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCC-CCCHHHHHHHHHHh----CCCccceeeccccHHHhHhhhhhh
Confidence            578999999999999999999999 59999998888887    799999999999999999987654
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {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
>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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]} 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
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} 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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure