Citrus Sinensis ID: 025634

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

MDRLRPRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKVTSSTNESKKGSDLPDACPPIKEHGSSQEPRGEKVPDVSEMEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRPTF

ccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccEEEHHHHccEEEEccccccEEEEEcccccccccHHHHHHHHcccccccccccccccccccEEEEEEEEcccEEEEEEEEEEEEEcccccccEEEEEEEEEEccccEEEEcccEEEccccc

ccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccccEEcHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccHHHHHHHHHcccccccccEEEEEEcccccccccHEEHHHHHHHccccccccccEEEccccEEEEEEcccccEEEEEHEHHHHHHHHccccccEEEEEEEEcccccccEccHHHEcccccc

mdrlrprqrsvftgfTKTELEKMEKLLMESKDDLLSKEFCQKIAKSfscsagragkpvvkWTEVQSWFQsrqqdrptkvtsstneskkgsdlpdacppikehgssqeprgekvpdvsemefearsskdgawydVDMFLAHRFLDCGEAEVRVRFVgfgadedewVNVKNavrersvplepsdchklkvgghvlcfqerrdqgihyDAHIAEIHRRMHDIRGCRCLFLVrynhdnteERVRLRRLCCRPTF

mdrlrprqrsvftgftktelEKMEKLLMESKDDLLSKEFCQKIAKSfscsagragkpvVKWTEVQSwfqsrqqdrptkvtsstneskkgsdlpdacppikehgssqeprgekvpDVSEMEFEarsskdgawYDVDMFLAHRFLDCGEAEVRVRFVGfgadedewvnVKNAVrersvplepsdchklkvGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVrynhdnteervrlrrlccrptf

MDRLRPRQRSVFTGFtktelekmekllmeSKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPTKVTSSTNESKKGSDLPDACPPIKEHGSSQEPRGEKVPDVSEMEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTeervrlrrlccrPTF

*********************************LLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWF************************************************************GAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCC****

***************TKTELEKMEKLLMESKDDLLSKEFCQKIAKSF***********VKWTEVQSWFQ**************************************************EFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRP**

********RSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSW**************************DACPPIK*************************SKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRPTF

***********FTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQ****************************************PDVSEMEFEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVRLRRLCCRPT*

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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
Query		250
359475952		245	PREDICTED: uncharacterized protein LOC10	0.976	0.995	0.678	6e-93
449436892		245	PREDICTED: uncharacterized protein LOC10	0.928	0.946	0.686	5e-91
224142945		238	predicted protein [Populus trichocarpa]	0.952	1.0	0.698	5e-91
255550954		266	conserved hypothetical protein [Ricinus	0.944	0.887	0.672	4e-89
388516789		231	unknown [Lotus japonicus]	0.924	1.0	0.645	3e-84
356507935		231	PREDICTED: uncharacterized protein LOC10	0.872	0.943	0.628	9e-82
356515633		231	PREDICTED: uncharacterized protein LOC10	0.872	0.943	0.616	3e-81
255646545		231	unknown [Glycine max]	0.872	0.943	0.624	5e-81
225442489		247	PREDICTED: uncharacterized protein LOC10	0.944	0.955	0.535	5e-69
255549846		285	conserved hypothetical protein [Ricinus	0.936	0.821	0.536	4e-66

>gi\|359475952\|ref\|XP_002277697.2\| PREDICTED: uncharacterized protein LOC100245843 [Vitis vinifera] gi\|296081562\|emb\|CBI20567.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  346 bits (887), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 169/249 (67%), Positives = 198/249 (79%), Gaps = 5/249 (2%)

Query: 1   MDRLRPRQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVK 60
           MDRLRPR+R +F+GFTK E+EKMEK+L ES +  L+ +FC+++   F+ S+GRAGKP +K
Sbjct: 1   MDRLRPRERRLFSGFTKLEVEKMEKVLKESGEQALNPDFCKRLTGGFNRSSGRAGKPAIK 60

Query: 61  WTEVQSWFQSRQQDRPTKVTSSTNESKKGSDLPDACPPIKEHGSSQEPRGEKVPDVSEME 120
           W EVQSWFQ R Q+   KV+   N SK+   LP+  P  K H SSQ P      D+SE+E
Sbjct: 61  WIEVQSWFQDRLQECTHKVSCPPNVSKELCVLPETFPSNKLHESSQMPE-----DLSELE 115

Query: 121 FEARSSKDGAWYDVDMFLAHRFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEP 180
           FEARSSKDGAWYDVD FL HRFL  GE EVRVRFVGFGA+EDEWVNVK AVRERS+PLE 
Sbjct: 116 FEARSSKDGAWYDVDTFLTHRFLSSGELEVRVRFVGFGAEEDEWVNVKKAVRERSLPLEH 175

Query: 181 SDCHKLKVGGHVLCFQERRDQGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNTEERVR 240
           S+CHK+KVG  VLCFQERRDQ I+YDAH+ EI R+MHDIRGCRCLFL+RY+HDNTEERV 
Sbjct: 176 SECHKVKVGDVVLCFQERRDQAIYYDAHVVEIQRKMHDIRGCRCLFLIRYDHDNTEERVH 235

Query: 241 LRRLCCRPT 249
           LRRLCCRPT
Sbjct: 236 LRRLCCRPT 244

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|449436892\|ref\|XP_004136226.1\| PREDICTED: uncharacterized protein LOC101218909 [Cucumis sativus] gi\|449519513\|ref\|XP_004166779.1\| PREDICTED: uncharacterized protein LOC101229999 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224142945\|ref\|XP_002324790.1\| predicted protein [Populus trichocarpa] gi\|222866224\|gb\|EEF03355.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255550954\|ref\|XP_002516525.1\| conserved hypothetical protein [Ricinus communis] gi\|223544345\|gb\|EEF45866.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

>gi\|388516789\|gb\|AFK46456.1\| unknown [Lotus japonicus]	Back alignment and taxonomy information

>gi\|356507935\|ref\|XP_003522718.1\| PREDICTED: uncharacterized protein LOC100817690 [Glycine max]	Back alignment and taxonomy information

>gi\|356515633\|ref\|XP_003526503.1\| PREDICTED: uncharacterized protein LOC100801021 [Glycine max]	Back alignment and taxonomy information

>gi\|255646545\|gb\|ACU23747.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|225442489\|ref\|XP_002283948.1\| PREDICTED: uncharacterized protein LOC100258357 [Vitis vinifera] gi\|297743205\|emb\|CBI36072.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255549846\|ref\|XP_002515974.1\| conserved hypothetical protein [Ricinus communis] gi\|223544879\|gb\|EEF46394.1\| conserved hypothetical protein [Ricinus communis]	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
Query		250
TAIR\|locus:1005716727		258	SHH1 "AT1G15215" [Arabidopsis	0.808	0.782	0.455	1e-45
TAIR\|locus:2095077		349	SHH2 "SAWADEE homeodomain homo	0.532	0.381	0.535	9.6e-44

TAIR\|locus:1005716727 SHH1 "AT1G15215" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 98/215 (45%), Positives = 132/215 (61%)

Query:    32 DDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSR--QQDRP-TKVTSS------ 82
             D  L K+FCQ +A +FSCS  R GK  + W +VQ WFQ +   Q +P +K   S      
Sbjct:    31 DQSLHKDFCQTVASTFSCSVNRNGKSSITWKQVQIWFQEKLKHQSQPKSKTLPSPPLQIH 90

Query:    83 --TNESKKGSDLPDACPPIKEHGSSQEPRGEKVPDVSEMEFEARSSKDGAWYDVDMFLAH 140
               +N S   S+  +A      + +  + R  K  D++++ FEA+S++D AWYDV  FL +
Sbjct:    91 DLSNPSSYASNASNAT--FVGNSTFVQTRKGKASDLADLAFEAKSARDYAWYDVSSFLTY 148

Query:   141 RFLDCGEAEVRVRFVGFGADEDEWVNVKNAVRERSVPLEPSDCHKLKVGGHVLCFQERRD 200
             R L  GE EVRVRF GF    DEWVNVK +VRERS+P+EPS+C ++ VG  +LCFQER D
Sbjct:   149 RVLRTGELEVRVRFSGFDNRHDEWVNVKTSVRERSIPVEPSECGRVNVGDLLLCFQERED 208

Query:   201 QGIHYDAHIAEIHRRMHDIRGCRCLFLVRYNHDNT 235
             Q ++ D H+  I R +HD   C C+FLVRY  DNT
Sbjct:   209 QALYCDGHVLNIKRGIHDHARCNCVFLVRYELDNT 243

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0006306 "DNA methylation" evidence=IMP

GO:0006346 "methylation-dependent chromatin silencing" evidence=IMP

GO:0033562 "cotranscriptional gene silencing by small RNA" evidence=IMP

TAIR\|locus:2095077 SHH2 "SAWADEE homeodomain homolog 2" [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

Your Input:
	grail3.0007011401	hypothetical protein (238 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		250
KOG0489		261	consensus Transcription factor zerknullt and relat	99.75
KOG0842		307	consensus Transcription factor tinman/NKX2-3, cont	99.72
KOG0488		309	consensus Transcription factor BarH and related HO	99.67
KOG0484		125	consensus Transcription factor PHOX2/ARIX, contain	99.62
KOG0487		308	consensus Transcription factor Abd-B, contains HOX	99.62
KOG0843		197	consensus Transcription factor EMX1 and related HO	99.61
KOG0492		246	consensus Transcription factor MSH, contains HOX d	99.58
PF00046		57	Homeobox: Homeobox domain not present here.; Inter	99.56
KOG0850		245	consensus Transcription factor DLX and related pro	99.53
KOG2251		228	consensus Homeobox transcription factor [Transcrip	99.49
smart00389		56	HOX Homeodomain. DNA-binding factors that are invo	99.48
KOG0485		268	consensus Transcription factor NKX-5.1/HMX1, conta	99.46
KOG0493		342	consensus Transcription factor Engrailed, contains	99.45
TIGR01565		58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.42
cd00086		59	homeodomain Homeodomain; DNA binding domains invol	99.42
KOG0491		194	consensus Transcription factor BSH, contains HOX d	99.35
KOG0494		332	consensus Transcription factor CHX10 and related H	99.33
KOG0844		408	consensus Transcription factor EVX1, contains HOX	99.3
KOG0848		317	consensus Transcription factor Caudal, contains HO	99.28
KOG0483		198	consensus Transcription factor HEX, contains HOX a	99.28
COG5576		156	Homeodomain-containing transcription factor [Trans	99.05
KOG0486		351	consensus Transcription factor PTX1, contains HOX	99.05
KOG0490		235	consensus Transcription factor, contains HOX domai	99.03
KOG0847		288	consensus Transcription factor, contains HOX domai	98.97
KOG4577		383	consensus Transcription factor LIM3, contains LIM	98.69
KOG0849		354	consensus Transcription factor PRD and related pro	98.67
KOG0775		304	consensus Transcription factor SIX and related HOX	98.09
KOG3802		398	consensus Transcription factor OCT-1, contains POU	98.09
PF05920		40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.04
KOG2252		558	consensus CCAAT displacement protein and related h	97.77
KOG0490		235	consensus Transcription factor, contains HOX domai	97.5
KOG0774		334	consensus Transcription factor PBX and related HOX	97.38
PF15057		124	DUF4537: Domain of unknown function (DUF4537)	96.27
PF11717		55	Tudor-knot: RNA binding activity-knot of a chromod	96.26
KOG1168		385	consensus Transcription factor ACJ6/BRN-3, contain	95.15
KOG1146		1406	consensus Homeobox protein [General function predi	95.02
cd00024		55	CHROMO Chromatin organization modifier (chromo) do	94.24
PF04218		53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.65
PF00385		55	Chromo: Chromo (CHRromatin Organisation MOdifier)	93.32
PF11569		56	Homez: Homeodomain leucine-zipper encoding, Homez;	93.16
KOG0773		342	consensus Transcription factor MEIS1 and related H	93.1
smart00333		57	TUDOR Tudor domain. Domain of unknown function pre	92.21
PLN00104		450	MYST -like histone acetyltransferase; Provisional	92.1
cd04508		48	TUDOR Tudor domains are found in many eukaryotic o	92.05
smart00561		96	MBT Present in Drosophila Scm, l(3)mbt, and verteb	91.5
smart00298		55	CHROMO Chromatin organization modifier domain.	91.39
PF02820		73	MBT: mbt repeat; InterPro: IPR004092 The function	89.78
smart00743		61	Agenet Tudor-like domain present in plant sequence	87.83
PF12148		85	DUF3590: Protein of unknown function (DUF3590); In	86.88
PF10668		60	Phage_terminase: Phage terminase small subunit; In	85.98
smart00333		57	TUDOR Tudor domain. Domain of unknown function pre	85.66
smart00743		61	Agenet Tudor-like domain present in plant sequence	84.5
PF05641		68	Agenet: Agenet domain; InterPro: IPR008395 This do	83.83
PF11717		55	Tudor-knot: RNA binding activity-knot of a chromod	82.0
PF12824		164	MRP-L20: Mitochondrial ribosomal protein subunit L	81.55
PF06003		264	SMN: Survival motor neuron protein (SMN); InterPro	81.49

>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]	Back alignment and domain information

Probab=99.75  E-value=1e-18  Score=157.87  Aligned_cols=58  Identities=22%  Similarity=0.402  Sum_probs=55.5

Q ss_pred             CCCCCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCC
Q 025634            7 RQRSVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRP   76 (250)
Q Consensus         7 ~~Rr~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~   76 (250)
                      -.||.||.||..||.||||+|+.  |+||++..|.+||..|+|+|          +|||||||||||||+
T Consensus       158 ~~kR~RtayT~~QllELEkEFhf--N~YLtR~RRiEiA~~L~LtE----------rQIKIWFQNRRMK~K  215 (261)
T KOG0489|consen  158 KSKRRRTAFTRYQLLELEKEFHF--NKYLTRSRRIEIAHALNLTE----------RQIKIWFQNRRMKWK  215 (261)
T ss_pred             CCCCCCcccchhhhhhhhhhhcc--ccccchHHHHHHHhhcchhH----------HHHHHHHHHHHHHHH
Confidence            35779999999999999999999  79999999999999999998          999999999999998

>KOG0842 consensus Transcription factor tinman/NKX2-3, 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

>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]	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

>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]	Back alignment and domain information

>PF00046 Homeobox: Homeobox domain not present here	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

>KOG2251 consensus Homeobox transcription factor [Transcription]	Back alignment and domain information

>smart00389 HOX Homeodomain	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

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class	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

>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]	Back alignment and domain information

>COG5576 Homeodomain-containing transcription factor [Transcription]	Back alignment and domain information

>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]	Back alignment and domain information

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]	Back alignment and domain information

>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

>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]	Back alignment and domain information

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [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

>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]	Back alignment and domain information

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]	Back alignment and domain information

>PF15057 DUF4537: Domain of unknown function (DUF4537)	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

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]	Back alignment and domain information

>KOG1146 consensus Homeobox protein [General function prediction only]	Back alignment and domain information

>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

>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

>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

>smart00333 TUDOR Tudor domain	Back alignment and domain information

>PLN00104 MYST -like histone acetyltransferase; Provisional	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

>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2	Back alignment and domain information

>smart00298 CHROMO Chromatin organization modifier domain	Back alignment and domain information

>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression	Back alignment and domain information

>smart00743 Agenet Tudor-like domain present in plant sequences	Back alignment and domain information

>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length	Back alignment and domain information

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes	Back alignment and domain information

>smart00333 TUDOR Tudor domain	Back alignment and domain information

>smart00743 Agenet Tudor-like domain present in plant sequences	Back alignment and domain information

>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []	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

>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

>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
Query		250
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-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 = 41.0 bits (95), Expect = 3e-04
 Identities = 42/269 (15%), Positives = 91/269 (33%), Gaps = 84/269 (31%)

Query: 9   RSVFTGFTKTELEKMEKLLMESKDD----------LLSKEFCQKIAKSFSCSAGRAGKPV 58
           +S+ +   K E++     ++ SKD           LLSK+  +++ + F        +  
Sbjct: 43  KSILS---KEEIDH----IIMSKDAVSGTLRLFWTLLSKQ--EEMVQKF---VEEVLRIN 90

Query: 59  VKWTEVQSWFQSRQQDRPTKVTSSTNESKKGSDLPDACPPIKEHGSSQEPRGEKVPDVSE 118
            K+  + S  ++ Q+  P+ +T    E +    L +      ++      R +    + +
Sbjct: 91  YKF--LMSPIKTEQRQ-PSMMTRMYIEQR--DRLYNDNQVFAKY---NVSRLQPYLKLRQ 142

Query: 119 MEFEARSSK----DGAWYDVDMF------LAHRFLD-CGEAEVRVRFVGFGADEDEWVNV 167
              E R +K    DG      +       +A   LD C   +V+ +   F      W+N+
Sbjct: 143 ALLELRPAKNVLIDG------VLGSGKTWVA---LDVCLSYKVQCKM-DFKI---FWLNL 189

Query: 168 KNAVRERSVPLEP--SDCHKLKVGGHVLCFQERRDQGIHYDAHIAE------IHRRMH-- 217
           KN     +V LE      +++         +      I    H  +      +  + +  
Sbjct: 190 KNCNSPETV-LEMLQKLLYQID---PNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN 245

Query: 218 ------DIR----------GCRCLFLVRY 230
                 +++           C+ L   R+
Sbjct: 246 CLLVLLNVQNAKAWNAFNLSCKILLTTRF 274

PyMOL of 1vt4

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		250
1wh5_A		80	ZF-HD homeobox family protein; structural genomics	99.74
2cra_A		70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.74
2djn_A		70	Homeobox protein DLX-5; structural genomics, NPPSF	99.74
2dmt_A		80	Homeobox protein BARH-like 1; homeobox domain, thr	99.73
2cuf_A		95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.73
2vi6_A		62	Homeobox protein nanog; homeodomain, DNA-binding,	99.73
2da2_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.72
2dmu_A		70	Homeobox protein goosecoid; homeobox domain, three	99.72
2l7z_A		73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.71
2h1k_A		63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.71
2kt0_A		84	Nanog, homeobox protein nanog; homeodomain, struct	99.71
1bw5_A		66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.71
2hdd_A		61	Protein (engrailed homeodomain Q50K); DNA binding,	99.71
2da3_A		80	Alpha-fetoprotein enhancer binding protein; homeob	99.71
1ig7_A		58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.71
1akh_A		61	Protein (mating-type protein A-1); complex (TWO DN	99.7
2dms_A		80	Homeobox protein OTX2; homeobox domain, three heli	99.7
3rkq_A		58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.7
2e1o_A		70	Homeobox protein PRH; DNA binding protein, structu	99.7
1wh7_A		80	ZF-HD homeobox family protein; homeobox domain, st	99.7
2da1_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.7
1nk2_P		77	Homeobox protein VND; homeodomain, DNA-binding pro	99.69
1jgg_A		60	Segmentation protein EVEN-skipped; homeodomain, pr	99.69
2ly9_A		74	Zinc fingers and homeoboxes protein 1; structural	99.69
2cue_A		80	Paired box protein PAX6; homeobox domain, transcri	99.68
1ahd_P		68	Antennapedia protein mutant; DNA binding protein/D	99.68
1zq3_P		68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.68
1puf_A		77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.68
1yz8_P		68	Pituitary homeobox 2; DNA binding protein, transcr	99.68
2dmq_A		80	LIM/homeobox protein LHX9; homeobox domain, three	99.68
2da4_A		80	Hypothetical protein DKFZP686K21156; homeobox doma	99.68
1ftt_A		68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.68
2k40_A		67	Homeobox expressed in ES cells 1; thermostable hom	99.67
1fjl_A		81	Paired protein; DNA-binding protein, paired BOX, t	99.67
2m0c_A		75	Homeobox protein aristaless-like 4; structural gen	99.67
3a02_A		60	Homeobox protein aristaless; homeodomain, developm	99.67
3a01_A		93	Homeodomain-containing protein; homeodomain, prote	99.67
2dn0_A		76	Zinc fingers and homeoboxes protein 3; triple home	99.67
2r5y_A		88	Homeotic protein sex combs reduced; homeodomain; H	99.66
2hi3_A		73	Homeodomain-only protein; transcription; NMR {Mus	99.66
1b8i_A		81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.66
2ecb_A		89	Zinc fingers and homeoboxes protein 1; homeobox do	99.65
1uhs_A		72	HOP, homeodomain only protein; structural genomics	99.65
3a03_A		56	T-cell leukemia homeobox protein 2; homeodomain, d	99.65
1b72_A		97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.64
2da5_A		75	Zinc fingers and homeoboxes protein 3; homeobox do	99.64
2ecc_A		76	Homeobox and leucine zipper protein homez; homeobo	99.63
1du6_A		64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.63
3nar_A		96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.63
1x2n_A		73	Homeobox protein pknox1; homeobox domain, structur	99.61
1puf_B		73	PRE-B-cell leukemia transcription factor-1; homeod	99.61
2cqx_A		72	LAG1 longevity assurance homolog 5; homeodomain, D	99.61
1lfb_A		99	Liver transcription factor (LFB1); transcription r	99.59
1mnm_C		87	Protein (MAT alpha-2 transcriptional repressor); t	99.59
1b72_B		87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.59
1au7_A		146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.59
1k61_A		60	Mating-type protein alpha-2; protein-DNA complex,	99.59
2dmp_A		89	Zinc fingers and homeoboxes protein 2; homeobox do	99.59
1e3o_C		160	Octamer-binding transcription factor 1; transcript	99.58
1x2m_A		64	LAG1 longevity assurance homolog 6; homeobox domai	99.58
2dmn_A		83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.57
2l9r_A		69	Homeobox protein NKX-3.1; structural genomics, nor	99.57
2xsd_C		164	POU domain, class 3, transcription factor 1; trans	99.57
2d5v_A		164	Hepatocyte nuclear factor 6; transcription factor,	99.57
2da6_A		102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.57
3d1n_I		151	POU domain, class 6, transcription factor 1; prote	99.56
3nau_A		66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.56
2e19_A		64	Transcription factor 8; homeobox domain, structura	99.56
1le8_B		83	Mating-type protein alpha-2; matalpha2, isothermal	99.56
1wi3_A		71	DNA-binding protein SATB2; homeodomain, helix-turn	99.55
3l1p_A		155	POU domain, class 5, transcription factor 1; POU,	99.5
1ic8_A		194	Hepatocyte nuclear factor 1-alpha; transcription r	99.41
3k2a_A		67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.38
2h8r_A		221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.35
1mh3_A		421	Maltose binding-A1 homeodomain protein chimera; MA	99.26
2lk2_A		89	Homeobox protein TGIF1; NESG, structural genomics,	99.07
2da7_A		71	Zinc finger homeobox protein 1B; homeobox domain,	99.04
2nzz_A		37	Penetratin conjugated GAS (374-394) peptide; confo	98.04
3h8z_A		128	FragIle X mental retardation syndrome-related Pro;	97.27
3fdr_A		94	Tudor and KH domain-containing protein; TDRD2, str	96.43
3ask_A		226	E3 ubiquitin-protein ligase UHRF1; histone reader	96.27
2ro0_A		92	Histone acetyltransferase ESA1; HAT, chromodomain,	95.67
2eqm_A		88	PHD finger protein 20-like 1; structural genomics,	95.56
1wgs_A		133	MYST histone acetyltransferase 1; tudor domain, MY	95.44
3s6w_A		54	Tudor domain-containing protein 3; methylated argi	95.39
4hae_A		81	CDY-like 2, chromodomain Y-like protein 2; protein	95.16
2eko_A		87	Histone acetyltransferase htatip; chromo domain, h	95.04
3pnw_C		77	Tudor domain-containing protein 3; FAB, structural	94.92
2rnz_A		94	Histone acetyltransferase ESA1; HAT, chromodomain,	94.55
4a4f_A		64	SurviVal of motor neuron-related-splicing factor;	94.48
2lcc_A		76	AT-rich interactive domain-containing protein 4A;	94.35
3db3_A		161	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	94.26
1mhn_A		59	SurviVal motor neuron protein; SMN, SMA, spinal mu	94.26
2bud_A		92	Males-absent on the first protein; transferase, MO	94.17
2diq_A		110	Tudor and KH domain-containing protein; tudor doma	94.16
3oa6_A		110	MALE-specific lethal 3 homolog; chromodomain, MSL3	94.06
1g5v_A		88	SurviVal motor neuron protein 1; mRNA processing,	93.92
4a4f_A		64	SurviVal of motor neuron-related-splicing factor;	93.77
3pnw_C		77	Tudor domain-containing protein 3; FAB, structural	93.73
1g5v_A		88	SurviVal motor neuron protein 1; mRNA processing,	93.67
2equ_A		74	PHD finger protein 20-like 1; tudor domain, struct	93.62
1mhn_A		59	SurviVal motor neuron protein; SMN, SMA, spinal mu	93.59
3ntk_A		169	Maternal protein tudor; tudor domain, OB-fold, GER	93.53
2f5k_A		102	MORF-related gene 15 isoform 1; beta barrel, gene	93.39
2rsn_A		75	Chromo domain-containing protein 1; chromodomain,	93.11
3sd4_A		69	PHD finger protein 20; tudor domain, transcription	93.05
2d9t_A		78	Tudor domain-containing protein 3; structural geno	93.0
3s6w_A		54	Tudor domain-containing protein 3; methylated argi	92.85
1wjq_A		107	KIAA1798 protein; MBT domain, structural genomics,	91.91
3p8d_A		67	Medulloblastoma antigen MU-MB-50.72; tudor domain,	91.65
2ldm_A		81	Uncharacterized protein; PHF20, tudor domain, epig	90.5
4b9w_A		201	TDRD1, tudor domain-containing protein 1; replicat	90.47
3qii_A		85	PHD finger protein 20; tudor domain, structural ge	90.33
4b9x_A		226	TDRD1, tudor domain-containing protein 1; replicat	90.06
2d9t_A		78	Tudor domain-containing protein 3; structural geno	89.78
2rso_A		92	Chromatin-associated protein SWI6; chromodomain, s	89.39
2hqx_A		246	P100 CO-activator tudor domain; human P100 tudor d	89.07
1pfb_A		55	Polycomb protein; chromatin, histone methylation,	88.62
2lcc_A		76	AT-rich interactive domain-containing protein 4A;	88.43
2lrq_A		85	Protein MRG15, NUA4 complex subunit EAF3 homolog;	88.11
2ys9_A		70	Homeobox and leucine zipper protein homez; homeodo	88.36
3fdt_A		59	Chromobox protein homolog 5; chromobox homolog5, C	87.98
3h91_A		54	Chromobox protein homolog 2; human chromobox homol	87.89
3i91_A		54	Chromobox protein homolog 8; chromobox homolog 8,	87.64
1q3l_A		69	Heterochromatin protein 1; chromodomain, HP1, chro	87.63
3f2u_A		55	Chromobox protein homolog 1; human chromobox homol	87.48
3m9q_A		101	Protein MALE-specific lethal-3; chromodomain, MSL3	86.98
3m9p_A		110	MALE-specific lethal 3 homolog; chromodomain, MSL3	86.83
3fdr_A		94	Tudor and KH domain-containing protein; TDRD2, str	86.61
1wjr_A		127	KIAA1617 protein; MBT domain, structural genomics,	86.35
3g7l_A		61	Chromo domain-containing protein 1; chromodomain,	86.29
2f5k_A		102	MORF-related gene 15 isoform 1; beta barrel, gene	85.71
2dnt_A		78	Chromodomain protein, Y chromosome-like, isoform B	85.49
1pdq_A		72	Polycomb protein; methyllysine, chromodomain, poly	85.41
3lwe_A		62	M-phase phosphoprotein 8; MPP8, structural genomic	85.26
1g6z_A		70	CLR4 protein; transferase; NMR {Schizosaccharomyce	84.55
2kvm_A		74	Chromobox protein homolog 7; histone modification,	83.23
1ap0_A		73	Modifier protein 1; chromatin-binding, protein int	83.18
2d9u_A		74	Chromobox protein homolog 2 (isoform 2); chromobox	82.45
3i5g_B		153	Myosin regulatory light chain LC-2, mantle muscle;	81.99
3m9q_A		101	Protein MALE-specific lethal-3; chromodomain, MSL3	81.09
2k1b_A		73	Chromobox protein homolog 7; alpha/beta protein, c	80.74

>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

Probab=99.74  E-value=3.4e-18  Score=128.64  Aligned_cols=62  Identities=16%  Similarity=0.240  Sum_probs=56.6

Q ss_pred             CCCCCCCccCCHHHHHHHHHHHHhhC--CCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhcccCCC
Q 025634            6 PRQRSVFTGFTKTELEKMEKLLMESK--DDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQDRPT   77 (250)
Q Consensus         6 ~~~Rr~Rt~FT~~Ql~eLEk~f~~~~--~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k~~~   77 (250)
                      .+.||.||.||.+|+.+||+.|+..+  ++||+...+++||..++|++          +||++||||||+|++.
T Consensus        15 ~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~----------~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPR----------QVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCH----------HHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCc----------ccccCCccccCcCCCC
Confidence            34677899999999999999999854  68999999999999999998          9999999999999873

PyMOL of 1wh5

>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

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; 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

>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

>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

>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

>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

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_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

>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

>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

>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

>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

>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

>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

>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

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {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

>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

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}	Back alignment and structure

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}	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

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*	Back alignment and structure

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} 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

>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

>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

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}	Back alignment and structure

>1b72_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

>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

>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

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} 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

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>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

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}	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

>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

>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

>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

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*	Back alignment and structure

>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

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A	Back alignment and structure

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1	Back alignment and structure

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}	Back alignment and structure

>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

>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

>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

>2ro0_A Histone acetyltransferase ESA1; HAT, chromodomain, tudor domain, RNA binding, activator, chromatin regulator, transcription; NMR {Saccharomyces cerevisiae}	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

>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

>3s6w_A Tudor domain-containing protein 3; methylated arginine recognize, ISO-propanol, transcri; 1.78A {Homo sapiens} PDB: 3pmt_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

>2eko_A Histone acetyltransferase htatip; chromo domain, histone tail, chromatin organization modifier, structural genomics, NPPSFA; 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

>2rnz_A Histone acetyltransferase ESA1; HAT, chromodomain, tudor domain, RNA binding, activator, chromatin regulator, transcription; NMR {Saccharomyces cerevisiae}	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

>2lcc_A AT-rich interactive domain-containing protein 4A; chromobarrel domain, RBBP1, transcription; NMR {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

>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

>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

>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

>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

>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation; NMR {Homo sapiens} SCOP: b.34.9.1	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

>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

>1g5v_A SurviVal motor neuron protein 1; mRNA processing, translation; NMR {Homo sapiens} SCOP: b.34.9.1	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

>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

>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

>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

>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

>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

>3s6w_A Tudor domain-containing protein 3; methylated arginine recognize, ISO-propanol, transcri; 1.78A {Homo sapiens} PDB: 3pmt_A*	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

>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

>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

>4b9w_A TDRD1, tudor domain-containing protein 1; replication; HET: 2MR; 2.10A {Mus musculus}	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

>4b9x_A TDRD1, tudor domain-containing protein 1; replication; 2.80A {Mus musculus}	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

>2rso_A Chromatin-associated protein SWI6; chromodomain, silencing, chromosomal protein, Met transcription; NMR {Schizosaccharomyces pombe}	Back alignment and structure

>2hqx_A P100 CO-activator tudor domain; human P100 tudor domain, proteolytic fragment, PSI, structural genomics; 1.42A {Homo sapiens} SCOP: b.34.9.1 PDB: 2hqe_A 3omc_A* 3omg_A* 2o4x_A 2e6n_A 2o4x_B	Back alignment and structure

>1pfb_A Polycomb protein; chromatin, histone methylation, polycomb, chromodomain, peptide binding protein; HET: M3L; 1.40A {Drosophila melanogaster} SCOP: b.34.13.2	Back alignment and structure

>2lcc_A AT-rich interactive domain-containing protein 4A; chromobarrel domain, RBBP1, transcription; NMR {Homo sapiens}	Back alignment and structure

>2lrq_A Protein MRG15, NUA4 complex subunit EAF3 homolog; epigenetics, LID complex, transcription; NMR {Drosophila melanogaster}	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

>3fdt_A Chromobox protein homolog 5; chromobox homolog5, CBX5, structural GENO structural genomics consortium, SGC, centromere, nucleus, phosphoprotein; HET: M3L; 2.00A {Homo sapiens}	Back alignment and structure

>3h91_A Chromobox protein homolog 2; human chromobox homolog 2, CBX2, structural genomics, structural genomics consortium, SGC, chromatin regulator, D binding, nucleus; HET: M3L; 1.50A {Homo sapiens} SCOP: b.34.13.2 PDB: 2k28_A 3i8z_A	Back alignment and structure

>3i91_A Chromobox protein homolog 8; chromobox homolog 8, CBX8, structural genomics structural genomics consortium, SGC, chromatin regulator, N phosphoprotein, repressor; HET: M3L; 1.55A {Homo sapiens} SCOP: b.34.13.2 PDB: 3gv6_A* 3i90_A*	Back alignment and structure

>1q3l_A Heterochromatin protein 1; chromodomain, HP1, chromatin, methyllysine, monomethyllysine, structural protein; HET: MLZ; 1.64A {Drosophila melanogaster} SCOP: b.34.13.2 PDB: 1kne_A* 1kna_A*	Back alignment and structure

>3f2u_A Chromobox protein homolog 1; human chromobox homolog 1, CBX1, structural genomics, struct genomics consortium, SGC, centromere, nucleus; 1.80A {Homo sapiens} PDB: 3tzd_A* 2l11_A* 3dm1_A*	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

>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

>1wjr_A KIAA1617 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

>3g7l_A Chromo domain-containing protein 1; chromodomain, protein-peptide complex, silencing, cell cycle, chromosome partition, DNA-binding, nucleus; HET: M3L; 2.20A {Schizosaccharomyces pombe}	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

>2dnt_A Chromodomain protein, Y chromosome-like, isoform B; histone H3 tail, choromatin organization modifier, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: b.34.13.2	Back alignment and structure

>1pdq_A Polycomb protein; methyllysine, chromodomain, polycomb, lysine methylation, trimethyllysine, cation-PI, chromo, structural protein; HET: M3L; 1.76A {Drosophila melanogaster} SCOP: b.34.13.2	Back alignment and structure

>3lwe_A M-phase phosphoprotein 8; MPP8, structural genomics, structural genomics consortium, S repeat, nucleus, cell cycle; 2.05A {Homo sapiens} SCOP: b.34.13.0 PDB: 3r93_A* 3svm_A* 3qo2_A*	Back alignment and structure

>1g6z_A CLR4 protein; transferase; NMR {Schizosaccharomyces pombe} SCOP: b.34.13.2	Back alignment and structure

>2kvm_A Chromobox protein homolog 7; histone modification, lysine methylation, chromobox, polycom chromatin-binding; HET: MLY; NMR {Mus musculus}	Back alignment and structure

>1ap0_A Modifier protein 1; chromatin-binding, protein interaction motif, alpha+beta; NMR {Mus musculus} SCOP: b.34.13.2 PDB: 1guw_A*	Back alignment and structure

>2d9u_A Chromobox protein homolog 2 (isoform 2); chromobox homolog 2, chromo domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3i5g_B Myosin regulatory light chain LC-2, mantle muscle; rigor-like, squid, muscle myosin, contractIle protein; 2.60A {Todarodes pacificus} PDB: 3i5f_B 3i5h_B 3i5i_B	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

>2k1b_A Chromobox protein homolog 7; alpha/beta protein, chromatin regulator, nucleus, repressor, transcription, transcription regulation; NMR {Homo sapiens} PDB: 2l12_A* 2l1b_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		250
d1p7ia_		53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.79
d2craa1		58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.78
d1ig7a_		58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.76
d1jgga_		57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.74
d1vnda_		77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.74
d1zq3p1		67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.74
d2e1oa1		57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.74
d9anta_		56	Antennapedia Homeodomain {Drosophila melanogaster	99.73
d1fjla_		65	Paired protein {Fruit fly (Drosophila melanogaster	99.72
d1ftta_		68	Thyroid transcription factor 1 homeodomain {Rat (R	99.71
d1pufa_		77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.71
d1yz8p1		60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.7
d1ocpa_		67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.7
d1le8a_		53	Mating type protein A1 Homeodomain {Baker's yeast	99.7
d2cuea1		68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.7
d1wi3a_		71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.69
d2cufa1		82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.69
d1s7ea1		50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.68
d1b72a_		88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.68
d1bw5a_		66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.67
d1uhsa_		72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.67
d1wh7a_		80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.65
d1au7a1		58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.64
d1lfba_		78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.64
d1e3oc1		57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.61
d1pufb_		73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2ecba1		76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.54
d2ecca1		76	Homeobox-leucine zipper protein Homez {Human (Homo	99.52
d1x2ma1		52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.47
d1k61a_		60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.46
d1x2na1		62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.43
d2cqxa1		59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.42
d1wgsa_		133	Probable histone acetyltransferase MYST1 {Mouse (M	96.07
d2buda1		88	Putative histone acetyltransferase MOF {Fruit fly	96.05
d1mhna_		59	Survival motor neuron protein 1, smn {Human (Homo	95.11
d2diqa1		97	Tudor and KH domain-containing protein TDRKH {Huma	95.03
d2d9ta1		60	Tudor domain-containing protein 3, TDRD3 {Mouse (M	94.72
d2hqxa1		90	P100 co-activator, SND1 {Human (Homo sapiens) [Tax	93.84
d2dnta1		66	Chromodomain protein, Y-like isoform {Human (Homo	93.25
d1pfba_		55	Polycomb protein, Pc {Fruit fly (Drosophila melano	92.92
d1q3la_		52	Heterochromatin protein 1, HP1 {Fruit fly (Drosoph	91.61
d2d9ta1		60	Tudor domain-containing protein 3, TDRD3 {Mouse (M	91.34
d1mhna_		59	Survival motor neuron protein 1, smn {Human (Homo	91.06
d1wjqa_		107	Lethal(3)malignant brain tumor-like 3 protein, L3M	91.0
d2dnva1		52	Chromobox protein homolog 8 {Mouse (Mus musculus)	90.67
d2f5ka1		83	Mortality factor 4-like protein 1, MRG15 {Human (H	89.86
d2f5ka1		83	Mortality factor 4-like protein 1, MRG15 {Human (H	89.46
d1guwa_		73	Heterochromatin protein 1, HP1 {Mouse (Mus musculu	89.17
d1g6za_		70	Histone methyltransferase clr4, chromo domain {Fis	87.59
d1oz2a2		108	Lethal(3)malignant brain tumor-like protein {Human	87.47
d1oz2a1		110	Lethal(3)malignant brain tumor-like protein {Human	86.52
d1wjsa_		127	Lethal(3)malignant brain tumor-like 3 protein, L3M	85.85
d1oi1a1		103	Scml2 protein {Human (Homo sapiens) [TaxId: 9606]}	85.21
d1oz2a3		106	Lethal(3)malignant brain tumor-like protein {Human	84.86
d1oi1a2		104	Scml2 protein {Human (Homo sapiens) [TaxId: 9606]}	83.99
d1f54a_		77	Calmodulin {Baker's yeast (Saccharomyces cerevisia	82.83
d1ijwc_		47	HIN recombinase (DNA-binding domain) {Synthetic}	82.41
d2dy8a1		69	ATP-dependent helicase CHD1 (Chromo domain protein	82.4
d2pq3a1		73	Calmodulin {Rattus norvegicus [TaxId: 10116]}	80.77

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.79  E-value=4.5e-20  Score=128.17  Aligned_cols=53  Identities=17%  Similarity=0.422  Sum_probs=50.8

Q ss_pred             CCCccCCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHhCCCCcCCCCCccchhHHHHHHhhhccc
Q 025634           10 SVFTGFTKTELEKMEKLLMESKDDLLSKEFCQKIAKSFSCSAGRAGKPVVKWTEVQSWFQSRQQD   74 (250)
Q Consensus        10 r~Rt~FT~~Ql~eLEk~f~~~~~~y~~~~~rq~LA~~f~lS~~RaGK~~Vq~~QVk~WFQNRR~k   74 (250)
                      |+||.||++|+..||+.|+.  ++||+...|++||.++|||+          +||++||||||+|
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~--~~yp~~~~r~~LA~~lgL~~----------~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNE--NRYLTERRRQQLSSELGLNE----------AQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHH--CSSCCHHHHHHHHHHHTCCH----------HHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHH--CCCCCHHHHHHHHHHhCCCh----------HHhhhcccccCCC
Confidence            47899999999999999999  78999999999999999998          9999999999986

PyMOL of d1p7ia_

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>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

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {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

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {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

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	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

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}	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

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}	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

>d2buda1 b.34.13.3 (A:367-454) Putative histone acetyltransferase MOF {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	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

>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

>d2d9ta1 b.34.9.1 (A:8-67) Tudor domain-containing protein 3, TDRD3 {Mouse (Mus musculus) [TaxId: 10090]}	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

>d2dnta1 b.34.13.2 (A:8-73) Chromodomain protein, Y-like isoform {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

>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

>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

>d2dnva1 b.34.13.2 (A:7-58) Chromobox protein homolog 8 {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

>d1guwa_ b.34.13.2 (A:) Heterochromatin protein 1, HP1 {Mouse (Mus musculus), HP1 beta (MOD1, M31) [TaxId: 10090]}	Back information, alignment and structure

>d1g6za_ b.34.13.2 (A:) Histone methyltransferase clr4, chromo domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}	Back information, alignment and structure

>d1oz2a2 b.34.9.3 (A:314-421) Lethal(3)malignant brain tumor-like protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1oz2a1 b.34.9.3 (A:204-313) Lethal(3)malignant brain tumor-like protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wjsa_ 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

>d1oi1a1 b.34.9.3 (A:33-135) Scml2 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1oz2a3 b.34.9.3 (A:422-527) Lethal(3)malignant brain tumor-like protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1oi1a2 b.34.9.3 (A:140-243) Scml2 protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1f54a_ a.39.1.5 (A:) Calmodulin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}	Back information, alignment and structure

>d2dy8a1 b.34.13.2 (A:279-347) ATP-dependent helicase CHD1 (Chromo domain protein 1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2pq3a1 a.39.1.5 (A:3-75) Calmodulin {Rattus norvegicus [TaxId: 10116]}	Back information, alignment and structure