Citrus Sinensis ID: 016887

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-
MGRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPGRNVPQPVAAPIPIPMSASVPPTMPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSVMVDHQKTSADLSASTATRVTVSSAEMMHKQVNANIAQGAPLSHSFVSVPAQTVEPKNASASSGISSSNPAVPPGGAAVISGTAATTAATGHPS
cccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccEEEHHHHHHccccccccccEEEEEccccccccccccccccccccccccccccccccccccEEEEEEEccccEEEEEEEEEEEEEcccccccccEEEEEEEEccccEEEEcccEEEccccccHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
cccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccccEEcHHHHHHHHHHccHHcccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccEEEEEEccccccHHHHHHHHHcccccccccEEEEEEcccccccccEEEHHHHHHcccccccccccEEEccccEEEEEEcccccEEEEEHEHHHHHHHHccccccEEEEEEEEcccccccEccHHHHccccccHHHHHHHHHHHHHccHccccccccHHHHccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccEEEcccEEHHHHccccc
mgrppsnggpafrfnpaevTEMEGILQEHHNAMPSREILVALAEKfsesperkgKIMVQMKQVWNWFQNRRYAIRAKsikspgklnvtplarddstpgrnvpqpvaapipipmsasvpptmpasanvpsvstagraasesTFMEFEaksardgawYDVSAFLAqrnfdtadpeVQVRFagfgaeedEWVNIKRhvrqrslpceasecvavlpgdlilCFQEGKDQALYFDAHVLDAqrrrhdvrgcrcrflvrydhdqseeivplrkvcrrpetDYRLQQLHAMNdsvmvdhqktsadlsastaTRVTVSSAEMMHKQVNAniaqgaplshsfvsvpaqtvepknasassgisssnpavppggaavisgtaattaatghps
mgrppsnggpafrfnPAEVTEMEGILQEHHNAMPSREILVALAEKFsesperkgkIMVQMKQVWNWFQNRRYAIRaksikspgklnvtplarddstpgrnvPQPVAAPIPIPMSASVPPTMPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGfgaeedewVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLdaqrrrhdvrgCRCRFlvrydhdqseeivplrkvcrrPETDYRLQQLHAMNDSVMVDHQKTSADLSASTATRVTVSSAEMMHKQVNANIAQGAPLSHSFVSVPAQTVEPKNASASSGISSSNPAVPPGGAAVISGTAATTAATGHPS
MGRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPGRNvpqpvaapipipMSASVPPTMPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQrrrhdvrgcrcrFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSVMVDHQKTSADLsastatrvtvssaEMMHKQVNANIAQGAPLSHSFVSVPAQTVEPKNasassgisssNPAVPPggaavisgtaattaatgHPS
*************************************ILVAL************KIMVQMKQVWNWFQNRRYAIRAK*************************************************************************RDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQL****************************************************************************************************
**************NPAEVTEMEGILQEHHNAMPSREILVALAE**************QMKQVWNWFQN************************************************************************FMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRL*******************************************************************************************************
********GPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPGRNVPQPVAAPIPIPMSASVPPTMPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSVMVDHQ**************TVSSAEMMHKQVNANIAQGAPLSHSFVSVPAQ*******************VPPGGAAVISGT***********
********GPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYA*****************************************************************ESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSV**************************************************************************GAAVISGTAATTAATGHPS
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MGRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPGRNVPQPVAAPIPIPMSASVPPTMPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRRHDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSVMVDHQKTSADLSASTATRVTVSSAEMMHKQVNANIAQGAPLSHSFVSVPAQTVEPKNASASSGISSSNPAVPPGGAAVISGTAATTAATGHPS
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

No hits with e-value below 0.001 by BLAST

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

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query381
357516491375 hypothetical protein MTR_8g061040 [Medic 0.942 0.957 0.626 1e-136
356514643383 PREDICTED: uncharacterized protein LOC10 0.939 0.934 0.630 1e-133
255554650401 DNA binding protein, putative [Ricinus c 0.971 0.922 0.618 1e-133
302142941419 unnamed protein product [Vitis vinifera] 0.989 0.899 0.622 1e-129
224061280286 predicted protein [Populus trichocarpa] 0.750 1.0 0.755 1e-127
224114579290 predicted protein [Populus trichocarpa] 0.761 1.0 0.727 1e-126
225461574414 PREDICTED: uncharacterized protein LOC10 0.992 0.913 0.594 1e-123
297834744349 sequence-specific DNA binding protein [A 0.892 0.974 0.617 1e-122
22331151348 sequence-specific DNA binding transcript 0.895 0.979 0.612 1e-121
334185436346 sequence-specific DNA binding transcript 0.892 0.982 0.614 1e-120
>gi|357516491|ref|XP_003628534.1| hypothetical protein MTR_8g061040 [Medicago truncatula] gi|355522556|gb|AET03010.1| hypothetical protein MTR_8g061040 [Medicago truncatula] Back     alignment and taxonomy information
 Score =  492 bits (1266), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 237/378 (62%), Positives = 287/378 (75%), Gaps = 19/378 (5%)

Query: 1   MGRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQM 60
           MGRPPSNGGPAFRF   EVTEME IL EH+NAMP+R++L ALA+KFSESP+RKGKI VQM
Sbjct: 1   MGRPPSNGGPAFRFTQPEVTEMEAILSEHNNAMPARDVLQALADKFSESPDRKGKITVQM 60

Query: 61  KQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPGRNVPQPVAAPIPIPMSASVPPT 120
           KQVWNWFQN+RYAIRAKS K+P KLN+TP+ R D TPGR + QP A+PIP P +      
Sbjct: 61  KQVWNWFQNKRYAIRAKSSKTPAKLNITPMPRTDLTPGRIMTQPTASPIPAPSA------ 114

Query: 121 MPASANVPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQVRFAG 180
                   SV T  +AA E++ MEFEAKS RDGAWYDV+ FL+ R+ +++DPEV VRFAG
Sbjct: 115 --------SVQTTAKAAPENSVMEFEAKSGRDGAWYDVATFLSYRHLESSDPEVLVRFAG 166

Query: 181 FGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRR 240
           FG+EEDEW+N++++VR RSLPCE+SECVAVLPGDLILCFQEGK+QALYFDAHVLDAQRRR
Sbjct: 167 FGSEEDEWINVRKNVRPRSLPCESSECVAVLPGDLILCFQEGKEQALYFDAHVLDAQRRR 226

Query: 241 HDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDSVMVDHQKTSADLS 300
           HDVRGCRCRFLVRYDHDQSEEIVPLRK+CRRPETDYRL QLHA+ND+   D QK + D  
Sbjct: 227 HDVRGCRCRFLVRYDHDQSEEIVPLRKICRRPETDYRLHQLHAVNDAAPTDQQKIALDHP 286

Query: 301 ASTATRVTVSSAEMMHKQVN-ANIAQGAPLSHSFVSVPAQT--VEPKNASASSGISSSNP 357
           A+       + +EM+ KQ   ANI    P+  + VS+P Q+  V+P  A   + + + N 
Sbjct: 287 ANVHGARVTNPSEMVQKQQQIANIHIVTPVLQTNVSIPPQSMNVDPMKAETKADVQAGNS 346

Query: 358 AVPPGGAAVISGTAATTA 375
             P   +A  +G  AT++
Sbjct: 347 VTP--SSAAFTGIIATSS 362

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|356514643|ref|XP_003526014.1| PREDICTED: uncharacterized protein LOC100783895 [Glycine max] Back     alignment and taxonomy information
>gi|255554650|ref|XP_002518363.1| DNA binding protein, putative [Ricinus communis] gi|223542458|gb|EEF43999.1| DNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|302142941|emb|CBI20236.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224061280|ref|XP_002300405.1| predicted protein [Populus trichocarpa] gi|222847663|gb|EEE85210.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224114579|ref|XP_002316800.1| predicted protein [Populus trichocarpa] gi|222859865|gb|EEE97412.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225461574|ref|XP_002282864.1| PREDICTED: uncharacterized protein LOC100246907 [Vitis vinifera] Back     alignment and taxonomy information
>gi|297834744|ref|XP_002885254.1| sequence-specific DNA binding protein [Arabidopsis lyrata subsp. lyrata] gi|297331094|gb|EFH61513.1| sequence-specific DNA binding protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|22331151|ref|NP_188467.2| sequence-specific DNA binding transcription factor [Arabidopsis thaliana] gi|20260286|gb|AAM13041.1| unknown protein [Arabidopsis thaliana] gi|28059773|gb|AAO30091.1| unknown protein [Arabidopsis thaliana] gi|332642567|gb|AEE76088.1| sequence-specific DNA binding transcription factor [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|334185436|ref|NP_001189923.1| sequence-specific DNA binding transcription factor [Arabidopsis thaliana] gi|332642569|gb|AEE76090.1| sequence-specific DNA binding transcription factor [Arabidopsis thaliana] 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 ?
Query381
TAIR|locus:2095077349 SHH2 "SAWADEE homeodomain homo 0.771 0.842 0.642 2e-97
TAIR|locus:1005716727258 SHH1 "AT1G15215" [Arabidopsis 0.637 0.941 0.398 1.6e-38
TAIR|locus:2095077 SHH2 "SAWADEE homeodomain homolog 2" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 968 (345.8 bits), Expect = 2.0e-97, P = 2.0e-97
 Identities = 196/305 (64%), Positives = 227/305 (74%)

Query:     1 MGRPPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQM 60
             MGRPPSNGGPAFRF   EVTEME IL +H+ AMP R IL ALA+KFSESPERKGK++VQ 
Sbjct:     1 MGRPPSNGGPAFRFILPEVTEMEAILLQHNTAMPGRHILEALADKFSESPERKGKVVVQF 60

Query:    61 KQVWNWFQNRRYAIRAKSIKSPGKLNVTPLARDDSTPG--RNXXXXXXXXXXXXMSASVP 118
             KQ+WNWFQNRRYA+RA+  K+PGKLNV+ + R D  P   R+            M+ ++P
Sbjct:    61 KQIWNWFQNRRYALRARGNKAPGKLNVSSMPRMD-LPNQMRSVIQPLSVPKTTHMTGNLP 119

Query:   119 PTMPASAN--VPSVSTAGRAASESTFMEFEAKSARDGAWYDVSAFLAQRNFDTADPEVQV 176
                PA +   VP V  +G   S+++++EFEAKSARDGAWYDV AFLA RN +  DPEVQV
Sbjct:   120 GMTPAPSGSLVPGVMRSG---SDNSYLEFEAKSARDGAWYDVQAFLAHRNLEIGDPEVQV 176

Query:   177 RFAGFGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDA 236
             RFAGF  EEDEW+N+K+HVRQRSLPCEASECVAVL GDL+LCFQEGKDQALYFDA VLDA
Sbjct:   177 RFAGFEVEEDEWINVKKHVRQRSLPCEASECVAVLAGDLVLCFQEGKDQALYFDAIVLDA 236

Query:   237 QXXXXXXXXXXXXFLVRYDHDQSE-EIVPLRKVCRRPETDYRLQQLH-AMNDSVMVD-HQ 293
             Q            FLVRY HDQSE EIVPLRK+CRRPETDYRLQQLH A+ND    + HQ
Sbjct:   237 QRRRHDVRGCRCRFLVRYSHDQSEQEIVPLRKICRRPETDYRLQQLHNAVNDLANSNQHQ 296

Query:   294 KTSAD 298
               + D
Sbjct:   297 IPALD 301
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA
GO:0043565 "sequence-specific DNA binding" evidence=IEA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
TAIR|locus:1005716727 SHH1 "AT1G15215" [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

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query381
smart0038957 smart00389, HOX, Homeodomain 5e-06
cd0008659 cd00086, homeodomain, Homeodomain; DNA binding dom 8e-06
pfam0004657 pfam00046, Homeobox, Homeobox domain 3e-04
>gnl|CDD|197696 smart00389, HOX, Homeodomain Back     alignment and domain information 
 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 12/63 (19%)

Query: 13 RFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRY 72
           F P ++ E+E   Q++    PSRE    LA+K   S           +QV  WFQNRR 
Sbjct: 7  SFTPEQLEELEKEFQKNPY--PSREEREELAKKLGLSE----------RQVKVWFQNRRA 54

Query: 73 AIR 75
            +
Sbjct: 55 KWK 57

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes. 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|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 381
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.74
KOG0489261 consensus Transcription factor zerknullt and relat 99.73
KOG0488309 consensus Transcription factor BarH and related HO 99.72
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.65
KOG0843197 consensus Transcription factor EMX1 and related HO 99.59
KOG0850245 consensus Transcription factor DLX and related pro 99.57
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.56
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.54
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.53
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.49
KOG0493342 consensus Transcription factor Engrailed, contains 99.45
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.44
KOG2251228 consensus Homeobox transcription factor [Transcrip 99.42
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.41
KOG0491194 consensus Transcription factor BSH, contains HOX d 99.38
KOG0494332 consensus Transcription factor CHX10 and related H 99.37
KOG0844408 consensus Transcription factor EVX1, contains HOX 99.36
KOG0848317 consensus Transcription factor Caudal, contains HO 99.34
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.31
KOG0483198 consensus Transcription factor HEX, contains HOX a 99.26
KOG0847288 consensus Transcription factor, contains HOX domai 99.08
KOG0486351 consensus Transcription factor PTX1, contains HOX 99.06
COG5576156 Homeodomain-containing transcription factor [Trans 99.04
KOG0490235 consensus Transcription factor, contains HOX domai 99.03
KOG4577383 consensus Transcription factor LIM3, contains LIM 98.77
KOG0849354 consensus Transcription factor PRD and related pro 98.59
KOG3802398 consensus Transcription factor OCT-1, contains POU 98.3
KOG0775304 consensus Transcription factor SIX and related HOX 98.05
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 98.01
KOG0490235 consensus Transcription factor, contains HOX domai 97.72
KOG2252558 consensus CCAAT displacement protein and related h 97.68
KOG0774334 consensus Transcription factor PBX and related HOX 97.15
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 96.39
PF1171755 Tudor-knot: RNA binding activity-knot of a chromod 95.16
KOG1146 1406 consensus Homeobox protein [General function predi 95.09
PF15057124 DUF4537: Domain of unknown function (DUF4537) 93.87
KOG0773342 consensus Transcription factor MEIS1 and related H 93.65
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 91.45
cd0002455 CHROMO Chromatin organization modifier (chromo) do 90.06
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 90.01
smart0033357 TUDOR Tudor domain. Domain of unknown function pre 88.88
PLN00104 450 MYST -like histone acetyltransferase; Provisional 86.24
PF12824164 MRP-L20: Mitochondrial ribosomal protein subunit L 85.79
smart0029855 CHROMO Chromatin organization modifier domain. 84.73
PF0038555 Chromo: Chromo (CHRromatin Organisation MOdifier) 83.16
cd0450848 TUDOR Tudor domains are found in many eukaryotic o 82.44
smart0074361 Agenet Tudor-like domain present in plant sequence 81.92
smart0056196 MBT Present in Drosophila Scm, l(3)mbt, and verteb 80.99
PF06003264 SMN: Survival motor neuron protein (SMN); InterPro 80.71
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information 
Probab=99.74  E-value=2.2e-18  Score=167.98  Aligned_cols=69  Identities=26%  Similarity=0.329  Sum_probs=62.5

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhhhccCCCC
Q 016887            4 PPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRAKSIKSPG   83 (381)
Q Consensus         4 Pps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~~~~p~   83 (381)
                      +...|++|.-||+.||-|||+.|++  ++||+..+|+.||..|+|++          +||||||||||||.||+-.-...
T Consensus       150 ~~~kRKrRVLFSqAQV~ELERRFrq--QRYLSAPERE~LA~~LrLT~----------TQVKIWFQNrRYK~KR~~~dk~~  217 (307)
T KOG0842|consen  150 KRKKRKRRVLFSQAQVYELERRFRQ--QRYLSAPEREHLASSLRLTP----------TQVKIWFQNRRYKTKRQQKDKAL  217 (307)
T ss_pred             cccccccccccchhHHHHHHHHHHh--hhccccHhHHHHHHhcCCCc----------hheeeeeecchhhhhhhhhhhhh
Confidence            4467999999999999999999999  69999999999999999975          99999999999999998865544


Q ss_pred             C
Q 016887           84 K   84 (381)
Q Consensus        84 k   84 (381)
                      .
T Consensus       218 ~  218 (307)
T KOG0842|consen  218 E  218 (307)
T ss_pred             h
Confidence            3

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [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
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, 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
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM 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
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0775 consensus Transcription factor SIX 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
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>PF15057 DUF4537: Domain of unknown function (DUF4537) Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus 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
>smart00333 TUDOR Tudor domain Back     alignment and domain information
>PLN00104 MYST -like histone acetyltransferase; Provisional Back     alignment and domain information
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>smart00298 CHROMO Chromatin organization modifier domain Back     alignment and domain information
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation Back     alignment and domain information
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains Back     alignment and domain information
>smart00743 Agenet Tudor-like domain present in plant sequences Back     alignment and domain information
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2 Back     alignment and domain information
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins 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 ?
Query381
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-06
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 4e-04
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
 Score = 47.9 bits (113), Expect = 5e-06
 Identities = 51/360 (14%), Positives = 102/360 (28%), Gaps = 118/360 (32%)

Query: 20  TEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQ------MKQVWNWFQNRRYA 73
            E++ I+        +  +   L          K + MVQ      ++  + +  +    
Sbjct: 49  EEIDHIIMSKDAVSGTLRLFWTL--------LSKQEEMVQKFVEEVLRINYKFLMSP--- 97

Query: 74  IRAKSIKSPGKLNVTPLARDDSTPGRNVPQPVAAPIPIPMSASVPPTMPASANVPSVSTA 133
           I+ +  +      +    RD      N  Q  A                   NV      
Sbjct: 98  IKTEQRQPSMMTRMYIEQRD---RLYNDNQVFA-----KY------------NVS----- 132

Query: 134 GRAASESTFMEFE--AKSARDGAWYDV--------SAFLAQRNFDTA-DPEVQVRFAG-- 180
            R      +++        R      +        +  +A    D     +VQ +     
Sbjct: 133 -R---LQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-VAL---DVCLSYKVQCKMDFKI 184

Query: 181 FGAEEDEWVNIKRHVRQRSLPCEASECVAVLPGDLILCFQEGKDQALYFDAHVLDAQRRR 240
           F      W+N+K         C + E   VL     L +Q   +     D H  + + R 
Sbjct: 185 F------WLNLKN--------CNSPE--TVLEMLQKLLYQIDPNWTSRSD-HSSNIKLRI 227

Query: 241 HDVRGCRCRFLVRYDHDQSEEIVPLRKVCRRPETDYRLQQLHAMNDS--VMVDHQKTSAD 298
           H ++    R L    ++    +  L  V    +        +A N S  +++    T+  
Sbjct: 228 HSIQAELRRLLKSKPYENCLLV--LLNVQ-NAKA------WNAFNLSCKILL----TTRF 274

Query: 299 ------LSASTATRVTVS----------SAEMMHKQVNANIA-------QGAPLSHSFVS 335
                 LSA+T T +++              ++ K ++              P   S ++
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIA 334
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query381
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.76
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.73
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.73
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.73
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.73
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.73
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.73
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.72
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.72
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.72
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.72
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.72
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.71
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.71
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.71
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.71
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.71
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.7
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.7
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.7
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.7
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.7
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.69
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.69
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.69
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.69
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.69
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.69
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.68
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.68
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.68
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.68
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.68
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.68
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.68
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.68
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.68
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.67
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.67
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.67
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.67
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.66
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.66
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.66
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.65
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.65
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.65
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.65
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.65
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.63
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.62
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.62
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.61
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.61
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.61
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.6
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.6
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.6
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.59
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.59
2e19_A64 Transcription factor 8; homeobox domain, structura 99.59
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.59
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.58
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.58
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.56
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.56
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.55
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.55
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.54
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.49
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.47
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.46
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.35
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.27
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.24
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.13
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.06
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.41
3h8z_A128 FragIle X mental retardation syndrome-related Pro; 95.62
2ro0_A92 Histone acetyltransferase ESA1; HAT, chromodomain, 95.06
3ask_A226 E3 ubiquitin-protein ligase UHRF1; histone reader 94.94
2eko_A87 Histone acetyltransferase htatip; chromo domain, h 94.84
3fdr_A94 Tudor and KH domain-containing protein; TDRD2, str 94.74
2eqm_A88 PHD finger protein 20-like 1; structural genomics, 94.56
2rnz_A94 Histone acetyltransferase ESA1; HAT, chromodomain, 94.07
2bud_A92 Males-absent on the first protein; transferase, MO 93.26
1wgs_A133 MYST histone acetyltransferase 1; tudor domain, MY 93.26
4a4f_A64 SurviVal of motor neuron-related-splicing factor; 93.09
3oa6_A110 MALE-specific lethal 3 homolog; chromodomain, MSL3 92.93
2lcc_A76 AT-rich interactive domain-containing protein 4A; 92.37
2equ_A74 PHD finger protein 20-like 1; tudor domain, struct 91.78
3pnw_C77 Tudor domain-containing protein 3; FAB, structural 91.76
2diq_A110 Tudor and KH domain-containing protein; tudor doma 91.72
1g5v_A88 SurviVal motor neuron protein 1; mRNA processing, 91.59
1mhn_A59 SurviVal motor neuron protein; SMN, SMA, spinal mu 91.31
4hae_A81 CDY-like 2, chromodomain Y-like protein 2; protein 91.3
3db3_A161 E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA 90.8
2f5k_A102 MORF-related gene 15 isoform 1; beta barrel, gene 90.55
3s6w_A54 Tudor domain-containing protein 3; methylated argi 89.86
3s6w_A54 Tudor domain-containing protein 3; methylated argi 89.2
3ntk_A169 Maternal protein tudor; tudor domain, OB-fold, GER 88.94
1mhn_A59 SurviVal motor neuron protein; SMN, SMA, spinal mu 88.84
3p8d_A67 Medulloblastoma antigen MU-MB-50.72; tudor domain, 88.59
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 88.27
2rsn_A75 Chromo domain-containing protein 1; chromodomain, 87.52
2lrq_A85 Protein MRG15, NUA4 complex subunit EAF3 homolog; 87.27
2d9t_A78 Tudor domain-containing protein 3; structural geno 87.17
3sd4_A69 PHD finger protein 20; tudor domain, transcription 87.04
2d9t_A78 Tudor domain-containing protein 3; structural geno 86.56
1g5v_A88 SurviVal motor neuron protein 1; mRNA processing, 86.34
3qii_A85 PHD finger protein 20; tudor domain, structural ge 86.27
2ldm_A81 Uncharacterized protein; PHF20, tudor domain, epig 86.23
2lcc_A76 AT-rich interactive domain-containing protein 4A; 85.56
4a4f_A64 SurviVal of motor neuron-related-splicing factor; 85.08
2f5k_A102 MORF-related gene 15 isoform 1; beta barrel, gene 84.33
3pnw_C77 Tudor domain-containing protein 3; FAB, structural 83.93
3m9q_A101 Protein MALE-specific lethal-3; chromodomain, MSL3 82.48
1wjq_A107 KIAA1798 protein; MBT domain, structural genomics, 81.82
1wgs_A133 MYST histone acetyltransferase 1; tudor domain, MY 81.46
3fwb_A161 Cell division control protein 31; gene gating, com 81.31
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 81.07
2lv7_A100 Calcium-binding protein 7; metal binding protein; 80.65
3fdr_A94 Tudor and KH domain-containing protein; TDRD2, str 80.3
3m9p_A110 MALE-specific lethal 3 homolog; chromodomain, MSL3 80.16
>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
Probab=99.76  E-value=1.4e-18  Score=139.68  Aligned_cols=75  Identities=24%  Similarity=0.364  Sum_probs=69.7

Q ss_pred             CCCCCCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhC-----CCccccCCcccccchhHhhhhcchhhHhhhc
Q 016887            4 PPSNGGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFS-----ESPERKGKIMVQMKQVWNWFQNRRYAIRAKS   78 (381)
Q Consensus         4 Pps~~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfn-----lS~~RaGk~~Vq~kQVk~WFQNRR~K~Kkk~   78 (381)
                      .+..++.|+.||++||..||+.|+.  ++||+...|++||+.||     .+.+++|+..|+++||++||||||+|+|++.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~--~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~   81 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNE--NQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRA   81 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHH--CSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhc--CCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHh
Confidence            4466899999999999999999999  79999999999999999     7778889999999999999999999999988


Q ss_pred             cC
Q 016887           79 IK   80 (381)
Q Consensus        79 ~~   80 (381)
                      ..
T Consensus        82 ~~   83 (95)
T 2cuf_A           82 NI   83 (95)
T ss_dssp             HC
T ss_pred             hc
Confidence            64
>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
>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
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* 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
>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
>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
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} 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
>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
>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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Back     alignment and structure
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B* Back     alignment and structure
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Back     alignment and structure
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Back     alignment and structure
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>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
>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
>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
>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
>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
>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
>3h8z_A FragIle X mental retardation syndrome-related Pro; tudor domains, FXR2, structura genomics, structural genomics consortium, SGC; 1.92A {Homo sapiens} PDB: 3o8v_A 3kuf_A 2bkd_N* Back     alignment and structure
>2ro0_A Histone acetyltransferase ESA1; HAT, chromodomain, tudor domain, RNA binding, activator, chromatin regulator, transcription; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules, epigenetic regulation, trimethylaion of lysine residue, ligase-DNA binding protein; HET: M3L; 2.90A {Homo sapiens} Back     alignment and structure
>2eko_A Histone acetyltransferase htatip; chromo domain, histone tail, chromatin organization modifier, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3fdr_A Tudor and KH domain-containing protein; TDRD2, structural genomics, structural genomics consortium, SGC, alternative splicing, RNA-binding; 1.75A {Homo sapiens} SCOP: b.34.9.1 Back     alignment and structure
>2eqm_A PHD finger protein 20-like 1; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2jtf_A Back     alignment and structure
>2rnz_A Histone acetyltransferase ESA1; HAT, chromodomain, tudor domain, RNA binding, activator, chromatin regulator, transcription; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2bud_A Males-absent on the first protein; transferase, MOF, HAT, acetyl-transfer, dosage compensation complex, DCC, royal family; NMR {Drosophila melanogaster} SCOP: b.34.13.3 Back     alignment and structure
>1wgs_A MYST histone acetyltransferase 1; tudor domain, MYST family, struct genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.34.13.3 Back     alignment and structure
>4a4f_A SurviVal of motor neuron-related-splicing factor; RNA binding protein; HET: 2MR; NMR {Homo sapiens} PDB: 4a4h_A* Back     alignment and structure
>3oa6_A MALE-specific lethal 3 homolog; chromodomain, MSL3, histone H4 tail, DNA backbone recognitio methyllysine recognition, H4K20ME1; HET: DNA MLZ; 2.35A {Homo sapiens} PDB: 3ob9_A* Back     alignment and structure
>2lcc_A AT-rich interactive domain-containing protein 4A; chromobarrel domain, RBBP1, transcription; NMR {Homo sapiens} Back     alignment and structure
>2equ_A PHD finger protein 20-like 1; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>3pnw_C Tudor domain-containing protein 3; FAB, structural genomics consortium, antibody, SGC, protein immune system complex; 2.05A {Homo sapiens} Back     alignment and structure
>2diq_A Tudor and KH domain-containing protein; tudor domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: b.34.9.1 Back     alignment and structure
>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation; NMR {Homo sapiens} SCOP: b.34.9.1 Back     alignment and structure
>1mhn_A SurviVal motor neuron protein; SMN, SMA, spinal muscular atrophy, RNA binding protein; 1.80A {Homo sapiens} SCOP: b.34.9.1 PDB: 4a4e_A* 4a4g_A* Back     alignment and structure
>4hae_A CDY-like 2, chromodomain Y-like protein 2; protein binding, structural genomics consortiu; 2.00A {Homo sapiens} Back     alignment and structure
>3db3_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, tandem tudor domains, LI metal binding, DNA replication; HET: M3L; 2.40A {Homo sapiens} PDB: 3db4_A 2l3r_A* Back     alignment and structure
>2f5k_A MORF-related gene 15 isoform 1; beta barrel, gene regulation; 2.20A {Homo sapiens} SCOP: b.34.13.3 PDB: 2efi_A Back     alignment and structure
>3s6w_A Tudor domain-containing protein 3; methylated arginine recognize, ISO-propanol, transcri; 1.78A {Homo sapiens} PDB: 3pmt_A* Back     alignment and structure
>3s6w_A Tudor domain-containing protein 3; methylated arginine recognize, ISO-propanol, transcri; 1.78A {Homo sapiens} PDB: 3pmt_A* Back     alignment and structure
>3ntk_A Maternal protein tudor; tudor domain, OB-fold, GERM cell formation, transcription; 1.80A {Drosophila melanogaster} PDB: 3nth_A* 3nti_A* Back     alignment and structure
>1mhn_A SurviVal motor neuron protein; SMN, SMA, spinal muscular atrophy, RNA binding protein; 1.80A {Homo sapiens} SCOP: b.34.9.1 PDB: 4a4e_A* 4a4g_A* Back     alignment and structure
>3p8d_A Medulloblastoma antigen MU-MB-50.72; tudor domain, lysine-methylated P53 binding, histone binding binding; 2.00A {Homo sapiens} 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
>2rsn_A Chromo domain-containing protein 1; chromodomain, protein-peptide complex, RNA-mediated gene SIL chromosomal protein, methylation; HET: M3L; NMR {Schizosaccharomyces pombe} Back     alignment and structure
>2lrq_A Protein MRG15, NUA4 complex subunit EAF3 homolog; epigenetics, LID complex, transcription; NMR {Drosophila melanogaster} Back     alignment and structure
>2d9t_A Tudor domain-containing protein 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: b.34.9.1 Back     alignment and structure
>3sd4_A PHD finger protein 20; tudor domain, transcription; 1.93A {Homo sapiens} PDB: 3q1j_A Back     alignment and structure
>2d9t_A Tudor domain-containing protein 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: b.34.9.1 Back     alignment and structure
>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation; NMR {Homo sapiens} SCOP: b.34.9.1 Back     alignment and structure
>3qii_A PHD finger protein 20; tudor domain, structural genomics, structural GE consortium, SGC, transcription regulator; 2.30A {Homo sapiens} Back     alignment and structure
>2ldm_A Uncharacterized protein; PHF20, tudor domain, epigenetics, methylated P53, transcript factor, transcription-protein binding complex; HET: M2L; NMR {Homo sapiens} Back     alignment and structure
>2lcc_A AT-rich interactive domain-containing protein 4A; chromobarrel domain, RBBP1, transcription; NMR {Homo sapiens} Back     alignment and structure
>4a4f_A SurviVal of motor neuron-related-splicing factor; RNA binding protein; HET: 2MR; NMR {Homo sapiens} PDB: 4a4h_A* Back     alignment and structure
>2f5k_A MORF-related gene 15 isoform 1; beta barrel, gene regulation; 2.20A {Homo sapiens} SCOP: b.34.13.3 PDB: 2efi_A Back     alignment and structure
>3pnw_C Tudor domain-containing protein 3; FAB, structural genomics consortium, antibody, SGC, protein immune system complex; 2.05A {Homo sapiens} Back     alignment and structure
>3m9q_A Protein MALE-specific lethal-3; chromodomain, MSL3, methyllysine recognition, aromatic CAGE, complex, transcription upregulation; 1.29A {Drosophila melanogaster} SCOP: b.34.13.0 Back     alignment and structure
>1wjq_A KIAA1798 protein; MBT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: b.34.9.3 Back     alignment and structure
>1wgs_A MYST histone acetyltransferase 1; tudor domain, MYST family, struct genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: b.34.13.3 Back     alignment and structure
>3fwb_A Cell division control protein 31; gene gating, complex, cell cycle, cell division, mitosis, MR transport, nuclear pore complex, nucleus, phosphoprotein; 2.50A {Saccharomyces cerevisiae} SCOP: a.39.1.5 PDB: 2gv5_A 2doq_A 3fwc_A Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure
>2lv7_A Calcium-binding protein 7; metal binding protein; NMR {Homo sapiens} Back     alignment and structure
>3fdr_A Tudor and KH domain-containing protein; TDRD2, structural genomics, structural genomics consortium, SGC, alternative splicing, RNA-binding; 1.75A {Homo sapiens} SCOP: b.34.9.1 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 381
d1k61a_60 a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast 4e-06
d1x2na162 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H 3e-05
d2cufa182 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM 9e-05
d1lfba_78 a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN 1e-04
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 4e-04
d1bw5a_66 a.4.1.1 (A:) Insulin gene enhancer protein isl-1 { 7e-04
d1le8a_53 a.4.1.1 (A:) Mating type protein A1 Homeodomain {B 7e-04
d2e1oa157 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo 0.001
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 0.002
d1p7ia_53 a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel 0.003
d1yz8p160 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo 0.003
d9anta_56 a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila 0.004
d1au7a158 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra 0.004
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.7 bits (98), Expect = 4e-06
 Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 13/68 (19%)

Query: 13 RFNPAEVTEMEGILQEH-HNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRR 71
          RF    V  +E    ++  N     + L  L +             +   Q+ NW  NRR
Sbjct: 4  RFTKENVRILESWFAKNIENPYLDTKGLENLMKN----------TSLSRIQIKNWVSNRR 53

Query: 72 YAIRAKSI 79
             + K+I
Sbjct: 54 R--KEKTI 59
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62 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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Length = 78 Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 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
>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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57 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
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53 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
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56 Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query381
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.76
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.76
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.75
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.75
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.74
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.74
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.74
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.73
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.71
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.71
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.71
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.7
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.69
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.68
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.68
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.68
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.67
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.66
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.64
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.64
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.64
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.64
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.62
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.62
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.61
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.6
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.59
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.57
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.47
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.46
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.4
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.38
d2buda188 Putative histone acetyltransferase MOF {Fruit fly 95.65
d1wgsa_133 Probable histone acetyltransferase MYST1 {Mouse (M 95.26
d2diqa197 Tudor and KH domain-containing protein TDRKH {Huma 92.13
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 89.29
d2dnta166 Chromodomain protein, Y-like isoform {Human (Homo 88.98
d2d9ta160 Tudor domain-containing protein 3, TDRD3 {Mouse (M 88.28
d1mhna_59 Survival motor neuron protein 1, smn {Human (Homo 88.13
d2hqxa190 P100 co-activator, SND1 {Human (Homo sapiens) [Tax 87.14
d1mhna_59 Survival motor neuron protein 1, smn {Human (Homo 86.59
d2d9ta160 Tudor domain-containing protein 3, TDRD3 {Mouse (M 85.66
d2f5ka183 Mortality factor 4-like protein 1, MRG15 {Human (H 85.47
d2f5ka183 Mortality factor 4-like protein 1, MRG15 {Human (H 82.96
d1pfba_55 Polycomb protein, Pc {Fruit fly (Drosophila melano 81.51
d1q3la_52 Heterochromatin protein 1, HP1 {Fruit fly (Drosoph 81.2
d2dnva152 Chromobox protein homolog 8 {Mouse (Mus musculus) 80.92
d1wjqa_107 Lethal(3)malignant brain tumor-like 3 protein, L3M 80.43
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.1e-19  Score=133.92  Aligned_cols=57  Identities=21%  Similarity=0.320  Sum_probs=54.3

Q ss_pred             CCCccccCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCccccCCcccccchhHhhhhcchhhHhh
Q 016887            8 GGPAFRFNPAEVTEMEGILQEHHNAMPSREILVALAEKFSESPERKGKIMVQMKQVWNWFQNRRYAIRA   76 (381)
Q Consensus         8 ~~pRtrFT~~QI~eLEk~F~e~~n~Yp~r~~rq~LA~kfnlS~~RaGk~~Vq~kQVk~WFQNRR~K~Kk   76 (381)
                      +++|+.||++|+..||+.|..  ++||+.+.|++||+.+||++          +||++||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~--~~yp~~~~r~~LA~~l~l~~----------~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAA--NKFITKDKRRKISAATSLSE----------RQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHH--CSSCCHHHHHHHHHHTCCCH----------HHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhh--cCCCCHHHHHHHHHHcCCCH----------HHeeecccchhhhccC
Confidence            678999999999999999999  79999999999999999985          9999999999999875
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {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
>d1fjla_ a.4.1.1 (A:) Paired 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
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {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
>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
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>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
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2buda1 b.34.13.3 (A:367-454) Putative histone acetyltransferase MOF {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1wgsa_ b.34.13.3 (A:) Probable histone acetyltransferase MYST1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2diqa1 b.34.9.1 (A:8-104) Tudor and KH domain-containing protein TDRKH {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
>d2dnta1 b.34.13.2 (A:8-73) Chromodomain protein, Y-like isoform {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2d9ta1 b.34.9.1 (A:8-67) Tudor domain-containing protein 3, TDRD3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1mhna_ b.34.9.1 (A:) Survival motor neuron protein 1, smn {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hqxa1 b.34.9.1 (A:8-97) P100 co-activator, SND1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mhna_ b.34.9.1 (A:) Survival motor neuron protein 1, smn {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2d9ta1 b.34.9.1 (A:8-67) Tudor domain-containing protein 3, TDRD3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2f5ka1 b.34.13.3 (A:6-88) Mortality factor 4-like protein 1, MRG15 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2f5ka1 b.34.13.3 (A:6-88) Mortality factor 4-like protein 1, MRG15 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pfba_ b.34.13.2 (A:) Polycomb protein, Pc {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1q3la_ b.34.13.2 (A:) Heterochromatin protein 1, HP1 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2dnva1 b.34.13.2 (A:7-58) Chromobox protein homolog 8 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1wjqa_ b.34.9.3 (A:) Lethal(3)malignant brain tumor-like 3 protein, L3MBTL3 (KIAA1798) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure