Citrus Sinensis ID: 029411

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----
MSRSSAGTAASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMNGPEGDAAV
ccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHcccccccccccHHHHHHHHHHHHccccccHHHHHHHHccccccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccc
ccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccccEEEEEEcccccccccc
msrssagtaasrvgddpaLDQFMEAYCEMLTKYEQELtkpfkdasLFLSEIDAQLKTLtvssnisgqsgsseeeidvkdhcidplaedrdLKDQLLRRYSGSLGSLKQEFLKkkkkgklpKEARQLLLDWWsrhhrwpypsepqklalaestgldqkqINNWFINqrkrhwkpsedmqfndisimngpegdaav
msrssagtaasrvgddpalDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTltvssnisgqsgsseeeidvKDHCIDPLAEDRDLKDQLLRRYsgslgslkqeflkkkkkgklpkeARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKrhwkpsedmqfndisimngpegdaav
MSRSSAGTAASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVssnisgqsgsseeeiDVKDHCIDPLAEDRDLKDQllrrysgslgslkqeflkkkkkgklpkEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMNGPEGDAAV
*******************DQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTL******************************************************************QLLLDWWSRHHRWPYP******AL****GLDQKQINNWFINQRKR*************************
*****************ALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDA*********************************************************************ARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK**********************
*************GDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSS*************DVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMNGPEGDAAV
************VGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLT***********************DPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMN********
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MSRSSAGTAASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSNISGQSGSSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQFNDISIMNGPEGDAAV
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 ?
Query194 2.2.26 [Sep-21-2011]
P46608379 Homeobox protein SBH1 OS= yes no 0.917 0.469 0.724 1e-66
O22299355 Homeobox protein knotted- N/A no 0.850 0.464 0.747 2e-65
Q9M6D9383 Homeobox protein SHOOT ME N/A no 0.860 0.436 0.717 5e-63
Q38874382 Homeobox protein SHOOT ME yes no 0.860 0.437 0.713 1e-62
P46639398 Homeobox protein knotted- no no 0.927 0.452 0.597 6e-51
Q41853351 Homeobox protein rough sh N/A no 0.953 0.527 0.569 3e-49
Q41330355 Homeotic protein knotted- N/A no 0.922 0.504 0.591 6e-49
Q10ED2341 Homeobox protein knotted- yes no 0.768 0.436 0.602 6e-49
O04135397 Homeobox protein knotted- N/A no 0.912 0.445 0.584 1e-48
O04134398 Homeobox protein knotted- N/A no 0.912 0.444 0.584 1e-48
>sp|P46608|HSBH1_SOYBN Homeobox protein SBH1 OS=Glycine max GN=H1 PE=2 SV=1 Back     alignment and function desciption
 Score =  252 bits (643), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/185 (72%), Positives = 155/185 (83%), Gaps = 7/185 (3%)

Query: 1   MSRSSAGTAASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTV 60
           M+   A   +S +G+DPALDQFMEAYCEMLTKYEQEL+KP K+A LFL  I+ Q K LT+
Sbjct: 167 MAGGDAAAGSSCIGEDPALDQFMEAYCEMLTKYEQELSKPLKEAMLFLQRIECQFKNLTI 226

Query: 61  SS-----NISG-QSGSSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKK 114
           SS     N  G ++GSSEE++D+ +  IDP AEDRDLK QLLR+YSG LGSLKQEF+KK+
Sbjct: 227 SSSDFASNEGGDRNGSSEEDVDLHN-MIDPQAEDRDLKGQLLRKYSGYLGSLKQEFMKKR 285

Query: 115 KKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPS 174
           KKGKLPKEARQ LL+WW+RH++WPYPSE QKLALAESTGLDQKQINNWFINQRKRHWKPS
Sbjct: 286 KKGKLPKEARQQLLEWWNRHYKWPYPSESQKLALAESTGLDQKQINNWFINQRKRHWKPS 345

Query: 175 EDMQF 179
           EDMQF
Sbjct: 346 EDMQF 350
Possible transcription activator involved in early embryonic development. Probably binds to the DNA sequence 5'-TGAC-3'.
Glycine max (taxid: 3847)
>sp|O22299|LET6_SOLLC Homeobox protein knotted-1-like LET6 OS=Solanum lycopersicum GN=LET6 PE=2 SV=1 Back     alignment and function description
>sp|Q9M6D9|STM_BRAOL Homeobox protein SHOOT MERISTEMLESS OS=Brassica oleracea GN=STM PE=2 SV=1 Back     alignment and function description
>sp|Q38874|STM_ARATH Homeobox protein SHOOT MERISTEMLESS OS=Arabidopsis thaliana GN=STM PE=1 SV=2 Back     alignment and function description
>sp|P46639|KNAT1_ARATH Homeobox protein knotted-1-like 1 OS=Arabidopsis thaliana GN=KNAT1 PE=1 SV=1 Back     alignment and function description
>sp|Q41853|RSH1_MAIZE Homeobox protein rough sheath 1 OS=Zea mays GN=RS1 PE=2 SV=1 Back     alignment and function description
>sp|Q41330|KN1_SOLLC Homeotic protein knotted-1 OS=Solanum lycopersicum GN=KN1 PE=2 SV=1 Back     alignment and function description
>sp|Q10ED2|KNOS8_ORYSJ Homeobox protein knotted-1-like 8 OS=Oryza sativa subsp. japonica GN=OSH43 PE=2 SV=1 Back     alignment and function description
>sp|O04135|KNAP2_MALDO Homeobox protein knotted-1-like 2 OS=Malus domestica PE=2 SV=1 Back     alignment and function description
>sp|O04134|KNAP1_MALDO Homeobox protein knotted-1-like 1 OS=Malus domestica PE=2 SV=1 Back     alignment and function description

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query194
285804239 383 class I KNOX homeobox transcription fact 0.860 0.436 0.754 2e-72
359485634 358 PREDICTED: homeobox protein SBH1-like, p 0.886 0.480 0.792 6e-71
110340603249 STM protein [Kalanchoe daigremontiana] 0.907 0.706 0.722 6e-71
147800378 359 hypothetical protein VITISV_033719 [Viti 0.886 0.479 0.792 7e-71
297739199248 unnamed protein product [Vitis vinifera] 0.886 0.693 0.792 4e-70
188528488 348 putative knotted-1-like protein [Heliant 0.860 0.479 0.734 6e-70
345649241 362 STM1 protein [Eschscholzia californica s 0.912 0.488 0.737 6e-69
63168778233 shoot meristemless-like protein [Eschsch 0.912 0.759 0.737 7e-69
225444460 361 PREDICTED: homeobox protein SBH1-like [V 0.886 0.476 0.764 2e-68
449434394 340 PREDICTED: homeobox protein SBH1-like [C 0.922 0.526 0.721 5e-68
>gi|285804239|gb|ADC35600.1| class I KNOX homeobox transcription factor STM-like 2 [Prunus persica] Back     alignment and taxonomy information
 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 132/175 (75%), Positives = 154/175 (88%), Gaps = 8/175 (4%)

Query: 13  VGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTVSSN----ISG-- 66
           +G+DPALDQFMEAYCEMLTKYEQEL+KPFK+A +FL  I++Q K LT+SS+    + G  
Sbjct: 179 LGEDPALDQFMEAYCEMLTKYEQELSKPFKEAMIFLQRIESQFKALTLSSSSDSAVCGDG 238

Query: 67  --QSGSSEEEIDVKDHCIDPLAEDRDLKDQLLRRYSGSLGSLKQEFLKKKKKGKLPKEAR 124
             ++GSSEEE+DV ++ IDP AEDR+LK QLLR+YSG LGSLKQEF+K++KKGKLPKEAR
Sbjct: 239 LDRNGSSEEEVDVNNNFIDPQAEDRELKGQLLRKYSGYLGSLKQEFMKERKKGKLPKEAR 298

Query: 125 QLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQF 179
           Q LLDWWSRH++WPYPSE QKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQF
Sbjct: 299 QQLLDWWSRHYKWPYPSESQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQF 353

Source: Prunus persica

Species: Prunus persica

Genus: Prunus

Family: Rosaceae

Order: Rosales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359485634|ref|XP_002273805.2| PREDICTED: homeobox protein SBH1-like, partial [Vitis vinifera] Back     alignment and taxonomy information
>gi|110340603|gb|ABG67974.1| STM protein [Kalanchoe daigremontiana] Back     alignment and taxonomy information
>gi|147800378|emb|CAN64264.1| hypothetical protein VITISV_033719 [Vitis vinifera] Back     alignment and taxonomy information
>gi|297739199|emb|CBI28850.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|188528488|emb|CAD58394.2| putative knotted-1-like protein [Helianthus tuberosus] Back     alignment and taxonomy information
>gi|345649241|gb|AEO14151.1| STM1 protein [Eschscholzia californica subsp. californica] Back     alignment and taxonomy information
>gi|63168778|gb|AAY34562.1| shoot meristemless-like protein [Eschscholzia californica subsp. californica] Back     alignment and taxonomy information
>gi|225444460|ref|XP_002271944.1| PREDICTED: homeobox protein SBH1-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|449434394|ref|XP_004134981.1| PREDICTED: homeobox protein SBH1-like [Cucumis sativus] gi|449518023|ref|XP_004166043.1| PREDICTED: homeobox protein SBH1-like [Cucumis sativus] 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 ?
Query194
TAIR|locus:2027089382 STM "SHOOT MERISTEMLESS" [Arab 0.907 0.460 0.520 3.8e-46
TAIR|locus:2128828398 KNAT1 "KNOTTED-like from Arabi 0.927 0.452 0.447 1.5e-37
TAIR|locus:2026810310 KNAT2 "KNOTTED-like from Arabi 0.860 0.538 0.443 9.2e-36
UNIPROTKB|P46609361 OSH1 "Homeobox protein knotted 0.845 0.454 0.441 1.3e-34
TAIR|locus:2146945431 KNAT3 "KNOTTED1-like homeobox 0.257 0.116 0.56 6.9e-19
TAIR|locus:2015554291 KNAT7 "KNOTTED-like homeobox o 0.237 0.158 0.630 1.9e-18
TAIR|locus:2184911393 KNAT4 "KNOTTED1-like homeobox 0.257 0.127 0.56 3.2e-17
TAIR|locus:2116632383 KNAT5 "KNOTTED1-like homeobox 0.257 0.130 0.56 3.9e-16
UNIPROTKB|A0A098934 GSM1 "Gamete-specific protein 0.252 0.052 0.612 7.1e-15
TAIR|locus:2018457290 BLH11 "BEL1-like homeodomain 1 0.288 0.193 0.483 6.9e-10
TAIR|locus:2027089 STM "SHOOT MERISTEMLESS" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 484 (175.4 bits), Expect = 3.8e-46, P = 3.8e-46
 Identities = 100/192 (52%), Positives = 117/192 (60%)

Query:     4 SSAGTAASR-----VGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTL 58
             S+A  AAS      +G+DP LDQFMEAYCEML KYEQEL+KPFK+A +FL  ++ Q K+L
Sbjct:   160 SAAAAAASMGPTGCLGEDPGLDQFMEAYCEMLVKYEQELSKPFKEAMVFLQRVECQFKSL 219

Query:    59 TVXXXXXXXXXXXXXXX-----------DVKDHCIDPLAEDRDLKDQXXXXXXXXXXXXX 107
             ++                          D+ +  +DP AEDR+LK Q             
Sbjct:   220 SLSSPSSFSGYGETAIDRNNNGSSEEEVDMNNEFVDPQAEDRELKGQLLRKYSGYLGSLK 279

Query:   108 XXXXXXXXXXXXXXEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQR 167
                           EARQ LLDWWSRH++WPYPSE QKLALAESTGLDQKQINNWFINQR
Sbjct:   280 QEFMKKRKKGKLPKEARQQLLDWWSRHYKWPYPSEQQKLALAESTGLDQKQINNWFINQR 339

Query:   168 KRHWKPSEDMQF 179
             KRHWKPSEDMQF
Sbjct:   340 KRHWKPSEDMQF 351
GO:0003677 "DNA binding" evidence=IEA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IEA;IDA
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0005515 "protein binding" evidence=IPI
GO:0019827 "stem cell maintenance" evidence=TAS
GO:0009934 "regulation of meristem structural organization" evidence=IMP
GO:0009691 "cytokinin biosynthetic process" evidence=TAS
GO:0048440 "carpel development" evidence=RCA;IMP
GO:0007389 "pattern specification process" evidence=RCA
GO:0009855 "determination of bilateral symmetry" evidence=RCA
GO:0009886 "post-embryonic morphogenesis" evidence=RCA
GO:0009887 "organ morphogenesis" evidence=RCA
GO:0009909 "regulation of flower development" evidence=RCA
GO:0010051 "xylem and phloem pattern formation" evidence=RCA
GO:0010093 "specification of floral organ identity" evidence=RCA
GO:0048438 "floral whorl development" evidence=RCA
GO:0048439 "flower morphogenesis" evidence=RCA
GO:0048481 "ovule development" evidence=RCA
GO:0048507 "meristem development" evidence=RCA
GO:0048513 "organ development" evidence=RCA
GO:0048519 "negative regulation of biological process" evidence=RCA
TAIR|locus:2128828 KNAT1 "KNOTTED-like from Arabidopsis thaliana" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2026810 KNAT2 "KNOTTED-like from Arabidopsis thaliana 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|P46609 OSH1 "Homeobox protein knotted-1-like 6" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2146945 KNAT3 "KNOTTED1-like homeobox gene 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2015554 KNAT7 "KNOTTED-like homeobox of Arabidopsis thaliana 7" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2184911 KNAT4 "KNOTTED1-like homeobox gene 4" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2116632 KNAT5 "KNOTTED1-like homeobox gene 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|A0A098 GSM1 "Gamete-specific protein minus 1" [Chlamydomonas reinhardtii (taxid:3055)] Back     alignment and assigned GO terms
TAIR|locus:2018457 BLH11 "BEL1-like homeodomain 11" [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) ?
P46608HSBH1_SOYBNNo assigned EC number0.72430.91750.4696yesno
Q38874STM_ARATHNo assigned EC number0.71340.86080.4371yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query194
pfam0379152 pfam03791, KNOX2, KNOX2 domain 4e-20
pfam0592040 pfam05920, Homeobox_KN, Homeobox KN domain 1e-17
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 6e-13
smart0038957 smart00389, HOX, Homeodomain 2e-12
pfam0378922 pfam03789, ELK, ELK domain 2e-05
pfam0004657 pfam00046, Homeobox, Homeobox domain 2e-04
>gnl|CDD|112597 pfam03791, KNOX2, KNOX2 domain Back     alignment and domain information 
 Score = 78.8 bits (195), Expect = 4e-20
 Identities = 27/49 (55%), Positives = 38/49 (77%)

Query: 11 SRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLT 59
            +G DP LDQFMEAYC++L KY++EL++PF +A  FL+EI+ QL+ L 
Sbjct: 3  RCIGADPELDQFMEAYCDVLVKYKEELSRPFDEAMTFLNEIETQLQNLC 51

The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerisation. Length = 52
>gnl|CDD|203350 pfam05920, Homeobox_KN, Homeobox KN domain Back     alignment and domain information
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information
>gnl|CDD|217729 pfam03789, ELK, ELK domain Back     alignment and domain information
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 194
PF0379152 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEIN 99.92
KOG0774334 consensus Transcription factor PBX and related HOX 99.9
KOG0773342 consensus Transcription factor MEIS1 and related H 99.88
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 99.75
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.63
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.6
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.6
KOG0775304 consensus Transcription factor SIX and related HOX 99.48
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.13
KOG0843197 consensus Transcription factor EMX1 and related HO 99.09
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.04
KOG0850245 consensus Transcription factor DLX and related pro 99.03
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.0
KOG0489261 consensus Transcription factor zerknullt and relat 98.92
KOG0493342 consensus Transcription factor Engrailed, contains 98.91
KOG3802398 consensus Transcription factor OCT-1, contains POU 98.87
COG5576156 Homeodomain-containing transcription factor [Trans 98.85
KOG0483198 consensus Transcription factor HEX, contains HOX a 98.82
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 98.8
KOG0491194 consensus Transcription factor BSH, contains HOX d 98.8
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 98.78
KOG0488309 consensus Transcription factor BarH and related HO 98.77
KOG0492246 consensus Transcription factor MSH, contains HOX d 98.75
KOG2251 228 consensus Homeobox transcription factor [Transcrip 98.65
KOG0494 332 consensus Transcription factor CHX10 and related H 98.54
KOG0486 351 consensus Transcription factor PTX1, contains HOX 98.48
KOG0848317 consensus Transcription factor Caudal, contains HO 98.45
KOG2252558 consensus CCAAT displacement protein and related h 98.34
KOG4577 383 consensus Transcription factor LIM3, contains LIM 98.33
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 98.09
KOG0849354 consensus Transcription factor PRD and related pro 98.08
KOG0490235 consensus Transcription factor, contains HOX domai 98.04
KOG0844 408 consensus Transcription factor EVX1, contains HOX 98.0
KOG0847288 consensus Transcription factor, contains HOX domai 97.98
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 97.86
KOG0773 342 consensus Transcription factor MEIS1 and related H 97.57
PF0378922 ELK: ELK domain ; InterPro: IPR005539 This domain 97.2
KOG0490235 consensus Transcription factor, contains HOX domai 96.22
KOG1146 1406 consensus Homeobox protein [General function predi 94.79
PF03792191 PBC: PBC domain; InterPro: IPR005542 Pbx proteins 94.13
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 93.04
PRK12516187 RNA polymerase sigma factor; Provisional 90.04
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 88.78
PRK11924179 RNA polymerase sigma factor; Provisional 88.64
PRK06811189 RNA polymerase factor sigma-70; Validated 88.32
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 87.74
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 87.7
PF0454550 Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763 85.48
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 84.91
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 82.7
PRK06759154 RNA polymerase factor sigma-70; Validated 80.19
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2 Back     alignment and domain information 
Probab=99.92  E-value=1.4e-25  Score=149.41  Aligned_cols=51  Identities=57%  Similarity=0.992  Sum_probs=49.3

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhhhhc
Q 029411           10 ASRVGDDPALDQFMEAYCEMLTKYEQELTKPFKDASLFLSEIDAQLKTLTV   60 (194)
Q Consensus        10 ~~~~~~dpeLd~fm~~Yc~~L~~y~~el~~p~~ea~~fl~~ie~ql~~L~~   60 (194)
                      ++++|+||||||||++||.||++|+++|++||+||+.||++||+||++||+
T Consensus         2 ~~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt~   52 (52)
T PF03791_consen    2 SSSIGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLTG   52 (52)
T ss_pred             CCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            578999999999999999999999999999999999999999999999984

KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 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
>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
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [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
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] 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
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0484 consensus Transcription factor PHOX2/ARIX, 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
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM 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
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins [] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins 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
>PRK12516 RNA polymerase sigma factor; Provisional 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
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated 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
>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
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription] 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
>PRK06759 RNA polymerase factor sigma-70; Validated 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 ?
Query194
3k2a_A67 Crystal Structure Of The Homeobox Domain Of Human H 3e-07
2dmn_A83 The Solution Structure Of The Homeobox Domain Of Hu 3e-06
4egc_A559 Crystal Structure Of Mbp-fused Human Six1 Bound To 7e-06
2lk2_A89 Solution Nmr Structure Of Homeobox Domain (171-248) 1e-05
1lfu_P82 Nmr Solution Stucture Of The Extended Pbx Homeodoma 3e-05
1x2n_A73 Solution Structure Of The Homeobox Domain Of Human 4e-05
1b72_B87 Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Le 5e-05
1du6_A64 Solution Structure Of The Truncated Pbx Homeodomain 7e-05
1puf_B73 Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bo 9e-05
1b8i_B63 Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX 1e-04
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox Protein Meis2 Length = 67 Back     alignment and structure 
Iteration: 1

 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 30/47 (63%)
Query: 130 WWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSED 176
           W  +H   PYPSE QK  LA+ TGL   Q+NNWFIN R+R  +P  D
Sbjct: 16  WLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXID 62
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Tgif2lx Length = 83 Back     alignment and structure
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human Eya2 Eya Domain Length = 559 Back     alignment and structure
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of Human Homeobox Protein Tgif1, Northeast Structural Genomics Consortium Target Hr4411b Length = 89 Back     alignment and structure
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain Bound To Dna Length = 82 Back     alignment and structure
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Pknox1 Length = 73 Back     alignment and structure
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX Length = 87 Back     alignment and structure
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain Length = 64 Back     alignment and structure
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna Length = 73 Back     alignment and structure
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX Length = 63 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 ?
Query194
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 3e-35
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 6e-35
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 1e-34
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 2e-34
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 2e-33
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 8e-32
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 1e-31
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 4e-26
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 9e-26
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 4e-25
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 3e-09
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 1e-06
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 2e-06
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 5e-06
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 2e-05
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 2e-05
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 4e-05
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 5e-05
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 1e-04
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 1e-04
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 3e-04
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 6e-04
>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* Length = 73 Back     alignment and structure
 Score =  117 bits (296), Expect = 3e-35
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWK 172
           ++K+    K+A ++L +++  H   PYPSE  K  LA+  G+   Q++NWF N+R R+ K
Sbjct: 2   RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61

Query: 173 PSEDMQ 178
                Q
Sbjct: 62  NIGKFQ 67
>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} Length = 83 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 Length = 73 Back     alignment and structure
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} Length = 67 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 Length = 87 Back     alignment and structure
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Length = 89 Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64 Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Length = 87 Back     alignment and structure
>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 Length = 60 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* Length = 83 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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164 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
>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
>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
>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
>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
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72 Back     alignment and structure
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76 Back     alignment and structure
>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
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96 Back     alignment and structure
>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 Length = 64 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query194
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.84
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.8
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.8
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.8
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.78
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.77
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.77
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.76
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.75
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.75
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.7
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.69
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.67
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.66
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.65
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.64
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.64
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.63
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.63
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.63
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.63
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.62
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.62
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.62
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.62
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.62
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.62
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.62
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.61
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.61
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.61
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.6
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.6
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.6
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.59
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.59
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.59
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.58
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.58
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.57
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.57
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.57
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.57
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.57
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.56
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.56
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.56
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.55
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.55
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.55
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.55
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.54
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.54
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.53
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.53
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.52
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.52
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.52
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.51
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.5
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.5
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.47
2e19_A64 Transcription factor 8; homeobox domain, structura 99.47
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.46
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.46
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.45
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.43
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.43
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.43
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.42
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.41
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.38
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.33
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.25
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.23
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.23
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.15
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 97.02
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 96.88
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 89.23
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 86.07
3c57_A95 Two component transcriptional regulatory protein; 84.44
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 81.89
2o8x_A70 Probable RNA polymerase sigma-C factor; promoter r 80.88
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 80.03
>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
Probab=99.84  E-value=3e-21  Score=139.01  Aligned_cols=68  Identities=43%  Similarity=0.669  Sum_probs=62.9

Q ss_pred             hhccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcCCCCCCcc
Q 029411          111 LKKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHWKPSEDMQ  178 (194)
Q Consensus       111 ~kkrkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~kk~~~~~~  178 (194)
                      .++++++.|++.++.+|+.||.+|..+|||+..+|..||..|||+..||.|||+|+|.|.|+++.+..
T Consensus         6 ~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~   73 (83)
T 2dmn_A            6 SGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQR   73 (83)
T ss_dssp             CCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhc
Confidence            46788899999999999999999999999999999999999999999999999999999998775443
>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
>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
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} Back     alignment and structure
>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
>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
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>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
>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
>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
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1 Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A 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
>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
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>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
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_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
>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
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>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
>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
>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
>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
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A 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
>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
>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

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 194
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 5e-22
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 2e-19
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 1e-17
d1x2ma152 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6e-08
d2cqxa159 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 6e-08
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 2e-07
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 5e-07
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 1e-06
d2ecba176 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote 2e-06
d1ocpa_67 a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus 3e-06
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 3e-05
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 4e-05
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 4e-05
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 4e-05
d1e3oc157 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human ( 4e-05
d1pufa_77 a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m 6e-05
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 6e-05
d1s7ea150 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M 6e-05
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 1e-04
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 1e-04
d2craa158 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human ( 1e-04
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 1e-04
d2cuea168 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H 2e-04
d1uhsa_72 a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse 2e-04
d1jgga_57 a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly ( 3e-04
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 6e-04
d2ecca176 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H 0.001
d1vnda_77 a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi 0.002
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 0.002
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.5 bits (204), Expect = 5e-22
 Identities = 26/58 (44%), Positives = 35/58 (60%)

Query: 112 KKKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKR 169
            K K+G LPK A  ++  W  +H   PYP+E +K  +A  T L   Q+NNWFIN R+R
Sbjct: 2   GKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRR 59
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 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
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80 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
>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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67 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
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66 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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 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
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77 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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58 Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72 Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57 Back     information, alignment and structure
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60 Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Length = 76 Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77 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

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query194
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.85
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.84
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.82
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.7
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.7
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.69
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.68
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.68
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.68
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.68
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.67
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.67
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.66
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.66
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.65
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.65
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.65
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.64
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.64
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.63
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.63
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.63
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.62
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.59
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.59
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.56
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.56
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.55
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.55
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.55
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.53
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.47
d1hlva166 DNA-binding domain of centromere binding protein B 90.64
d1rp3a271 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 87.34
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 83.91
d1or7a168 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 81.55
d2f66c165 Vacuolar protein sorting-associated protein 37, VP 80.13
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=4.8e-22  Score=134.82  Aligned_cols=59  Identities=44%  Similarity=0.791  Sum_probs=56.3

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChHHHhhhhHHHHhhcC
Q 029411          113 KKKKGKLPKEARQLLLDWWSRHHRWPYPSEPQKLALAESTGLDQKQINNWFINQRKRHW  171 (194)
Q Consensus       113 krkr~~l~k~~~~~L~~wf~~h~~~PYPs~~ek~~LA~~tgLt~~QV~nWF~N~R~R~k  171 (194)
                      |++|++||++++.+|+.||..|..||||+.+++..||..|||+.+||.|||+|+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            57788999999999999999999999999999999999999999999999999999864
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {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
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} 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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {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
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {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
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {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
>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
>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} 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
>d2f66c1 a.2.17.3 (C:142-206) Vacuolar protein sorting-associated protein 37, VPS37 (SRN2) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure