Citrus Sinensis ID: 027468

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---

MNSEIPETTAAAAVKFRGLNLDWTDMQQPIASFGTGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLLGKGHEDTNENSGDRKSENEITTESNERPSQIYVPSSDDRSRNIESTVIMKDFAATNVEEQTESSGNWCKFESGFLDETSSTLPWWELWS

ccccccccHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccc

cccccccccccccEEccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccc

mnseipetTAAAAVKFRglnldwtdmqqpiasfgtgnnkrrfsDEQVKSLEFMFesearpesrmkhrmadelglqpRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLlgkghedtnensgdrkseneittesnerpsqiyvpssddrsrnieSTVIMKDFAATNveeqtessgnwckfesgfldetsstlpwwelws

mnseipetTAAAAVKFRGLNLDWTDMQQPIasfgtgnnkrrFSDEQVKSLEFMfesearpesrMKHRMADELGLQPRQVaiwfqnkrarsktkqiereyTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLLgkghedtnensgdrkseneittesnerpsqiyvpssddrsrNIESTVIMKDFAATNVEEQTESSGNWCKFEsgfldetsstlpwwelws

MNSEIPETTAAAAVKFRGLNLDWTDMQQPIASFGTGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYELMRREHqlllvqlqklknllgkGHEDTNENSGDRKSENEITTESNERPSQIYVPSSDDRSRNIESTVIMKDFAATNVEEQTESSGNWCKFESGFLDETSSTLPWWELWS

***********AAVKFRGLNLDWTDMQQ************************************************RQVAIWFQN*************YTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLL****************************************************************GNWCKFESGFLDETSSTLPWWELW*

*******************************************DEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKR******************FETLAS***********************************************************************************************GFLDETSSTLPWWELWS

MNSEIPETTAAAAVKFRGLNLDWTDMQQPIASFGTGNNKRRFSDEQVKSLEFMFE***********RMADELGLQPRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLLGKG*************************SQIYVPSSDDRSRNIESTVIMKDFAATN********GNWCKFESGFLDETSSTLPWWELWS

****************************************RFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLL*******************************************************************************STLPWWELWS

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MNSEIPETTAAAAVKFRGLNLDWTDMQQPIASFGTGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQxxxxxxxxxxxxxxxxxxxxxFETLASSxxxxxxxxxxxxxxxxxxxxxLGKGHEDTNENSGDRKSENEITTESNERPSQIYVPSSDDRSRNIESTVIMKDFAATNVEEQTESSGNWCKFESGFLDETSSTLPWWELWS

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		223	2.2.26 [Sep-21-2011]
P46897		258	Homeobox-leucine zipper p	yes	no	0.838	0.724	0.390	1e-28
Q9M276		235	Homeobox-leucine zipper p	no	no	0.820	0.778	0.438	9e-28
Q651Z5		249	Homeobox-leucine zipper p	no	no	0.506	0.453	0.504	4e-26
Q9XH35		249	Homeobox-leucine zipper p	N/A	no	0.506	0.453	0.504	4e-26
Q6K498		277	Homeobox-leucine zipper p	no	no	0.475	0.382	0.490	1e-22
Q9XH37		277	Homeobox-leucine zipper p	N/A	no	0.475	0.382	0.490	1e-22
Q6Z248		269	Homeobox-leucine zipper p	no	no	0.632	0.524	0.408	5e-22
A2YWC0		269	Homeobox-leucine zipper p	N/A	no	0.632	0.524	0.408	5e-22
Q940J1		294	Homeobox-leucine zipper p	no	no	0.497	0.377	0.464	4e-21
Q10QP3		311	Homeobox-leucine zipper p	no	no	0.515	0.369	0.426	8e-21

>sp\|P46897\|ATHB7_ARATH Homeobox-leucine zipper protein ATHB-7 OS=Arabidopsis thaliana GN=ATHB-7 PE=2 SV=2	Back alignment and function desciption

 Score =  126 bits (317), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 89/228 (39%), Positives = 125/228 (54%), Gaps = 41/228 (17%)

Query: 37  NNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIE 96
           NN+RRFSDEQ+KSLE MFESE R E R K ++A ELGLQPRQVAIWFQNKRAR K+KQ+E
Sbjct: 31  NNQRRFSDEQIKSLEMMFESETRLEPRKKVQLARELGLQPRQVAIWFQNKRARWKSKQLE 90

Query: 97  REYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLL-GKGHEDTNENSGDR------K 149
            EY  L+  ++ LAS +E +++E Q L+ +LQ+LK     K  E+  + SGD+       
Sbjct: 91  TEYNILRQNYDNLASQFESLKKEKQALVSELQRLKEATQKKTQEEERQCSGDQAVVALSS 150

Query: 150 SENEITTESNER--PSQIY--VPSSDDRSR--------------NIESTVIMKDFAA--- 188
           + +E   E N R  P ++   +   DD+                N  S  I +++     
Sbjct: 151 THHESENEENRRRKPEEVRPEMEMKDDKGHHGVMCDHHDYEDDDNGYSNNIKREYFGGFE 210

Query: 189 ------TNVEEQTES----SGNWCKFESG---FLDETSSTLPWWELWS 223
                  N+ E  +S    S +W  F+S     LD++S+  PW + WS
Sbjct: 211 EEPDHLMNIVEPADSCLTSSDDWRGFKSDTTTLLDQSSNNYPWRDFWS 258

Probable transcription activator that may act as growth regulators in response to water deficit.
Arabidopsis thaliana (taxid: 3702)

>sp\|Q9M276\|ATB12_ARATH Homeobox-leucine zipper protein ATHB-12 OS=Arabidopsis thaliana GN=ATHB-12 PE=2 SV=1	Back alignment and function description

>sp\|Q651Z5\|HOX6_ORYSJ Homeobox-leucine zipper protein HOX6 OS=Oryza sativa subsp. japonica GN=HOX6 PE=2 SV=1	Back alignment and function description

>sp\|Q9XH35\|HOX6_ORYSI Homeobox-leucine zipper protein HOX6 OS=Oryza sativa subsp. indica GN=HOX6 PE=2 SV=2	Back alignment and function description

>sp\|Q6K498\|HOX4_ORYSJ Homeobox-leucine zipper protein HOX4 OS=Oryza sativa subsp. japonica GN=HOX4 PE=1 SV=1	Back alignment and function description

>sp\|Q9XH37\|HOX4_ORYSI Homeobox-leucine zipper protein HOX4 OS=Oryza sativa subsp. indica GN=HOX4 PE=1 SV=1	Back alignment and function description

>sp\|Q6Z248\|HOX20_ORYSJ Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. japonica GN=HOX20 PE=2 SV=1	Back alignment and function description

>sp\|A2YWC0\|HOX20_ORYSI Homeobox-leucine zipper protein HOX20 OS=Oryza sativa subsp. indica GN=HOX20 PE=2 SV=1	Back alignment and function description

>sp\|Q940J1\|ATB16_ARATH Homeobox-leucine zipper protein ATHB-16 OS=Arabidopsis thaliana GN=ATHB-16 PE=2 SV=2	Back alignment and function description

>sp\|Q10QP3\|HOX13_ORYSJ Homeobox-leucine zipper protein HOX13 OS=Oryza sativa subsp. japonica GN=HOX13 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		223
224053723		196	predicted protein [Populus trichocarpa]	0.780	0.887	0.505	2e-37
356520247		238	PREDICTED: homeobox-leucine zipper prote	0.838	0.785	0.447	6e-33
357514445		241	Homeobox-leucine zipper protein ATHB-7 [	0.816	0.755	0.441	6e-33
409191774		247	homeobox-leucine zipper protein [Medicag	0.816	0.736	0.446	1e-32
297742439		222	unnamed protein product [Vitis vinifera]	0.762	0.765	0.468	5e-32
225426584		192	PREDICTED: homeobox-leucine zipper prote	0.762	0.885	0.468	5e-32
147857129		192	hypothetical protein VITISV_026966 [Viti	0.771	0.895	0.457	7e-32
356559845		246	PREDICTED: LOW QUALITY PROTEIN: homeobox	0.771	0.699	0.453	1e-30
224130632		238	predicted protein [Populus trichocarpa]	0.816	0.764	0.421	1e-29
220702719		248	homeobox leucine zipper protein [Mirabil	0.820	0.737	0.426	2e-29

>gi\|224053723\|ref\|XP_002297947.1\| predicted protein [Populus trichocarpa] gi\|222845205\|gb\|EEE82752.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  161 bits (408), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 97/192 (50%), Positives = 127/192 (66%), Gaps = 18/192 (9%)

Query: 28  QPIASFGTGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKR 87
            P++S      KRRF+DEQ+K LEFMFESE+RPESR+K ++A ELGL+PRQVAIWFQN+R
Sbjct: 6   HPLSSIQKNAYKRRFTDEQIKFLEFMFESESRPESRVKQQLASELGLEPRQVAIWFQNRR 65

Query: 88  ARSKTKQIEREYTKLKAEFETLASSYELMRREHQLLLVQLQKLKNLLGKGHEDTN----- 142
           AR KTKQIE+EY+ LKA ++ LASS+E ++RE Q L++QL KLKN   K H   N     
Sbjct: 66  ARLKTKQIEKEYSILKASYDVLASSFESLKREKQSLIIQLHKLKNRHVKQHGSRNCGNQL 125

Query: 143 ENSGDRKSENEIT-TESNERPSQIY--------VPSSDDRSRNIESTVIMK-DFAATNVE 192
            +S D + EN+ T +ES E+PS            PSSD+  RN   TV M+ +    N  
Sbjct: 126 RSSRDGRFENKDTGSESKEKPSSPLDGNENEENRPSSDNNGRN---TVNMREEIDILNHT 182

Query: 193 EQTESSGNWCKF 204
           EQT++S  W +F
Sbjct: 183 EQTDNSSQWWEF 194

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356520247\|ref\|XP_003528775.1\| PREDICTED: homeobox-leucine zipper protein ATHB-7-like [Glycine max]	Back alignment and taxonomy information

>gi\|357514445\|ref\|XP_003627511.1\| Homeobox-leucine zipper protein ATHB-7 [Medicago truncatula] gi\|355521533\|gb\|AET01987.1\| Homeobox-leucine zipper protein ATHB-7 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|409191774\|gb\|AFV30231.1\| homeobox-leucine zipper protein [Medicago sativa]	Back alignment and taxonomy information

>gi\|297742439\|emb\|CBI34588.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225426584\|ref\|XP_002280048.1\| PREDICTED: homeobox-leucine zipper protein ATHB-12 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147857129\|emb\|CAN83496.1\| hypothetical protein VITISV_026966 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356559845\|ref\|XP_003548207.1\| PREDICTED: LOW QUALITY PROTEIN: homeobox-leucine zipper protein ATHB-7-like [Glycine max]	Back alignment and taxonomy information

>gi\|224130632\|ref\|XP_002320889.1\| predicted protein [Populus trichocarpa] gi\|222861662\|gb\|EEE99204.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|220702719\|gb\|ACL81158.1\| homeobox leucine zipper protein [Mirabilis jalapa]	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		223
TAIR\|locus:2062754		258	HB-7 "homeobox 7" [Arabidopsis	0.627	0.542	0.430	2.3e-29
TAIR\|locus:2079542		235	HB-12 "homeobox 12" [Arabidops	0.573	0.544	0.480	1.8e-25
TAIR\|locus:2140055		294	HB16 "homeobox protein 16" [Ar	0.793	0.602	0.362	9e-22
TAIR\|locus:2041283		311	HB6 "homeobox protein 6" [Arab	0.614	0.440	0.394	6.3e-21
TAIR\|locus:2202795		255	AtHB23 "homeobox protein 23" [	0.807	0.705	0.322	6.5e-19
TAIR\|locus:2046263		220	HB21 "homeobox protein 21" [Ar	0.313	0.318	0.614	1.4e-18
TAIR\|locus:2168225		312	HB5 "homeobox protein 5" [Arab	0.403	0.288	0.511	2.2e-18
TAIR\|locus:2084228		272	HB-1 "homeobox 1" [Arabidopsis	0.520	0.426	0.405	2.8e-18
TAIR\|locus:2205075		294	ATHB13 [Arabidopsis thaliana (	0.367	0.278	0.524	1.2e-17
TAIR\|locus:2150901		314	HB-3 "homeobox 3" [Arabidopsis	0.811	0.576	0.308	1.6e-17

TAIR\|locus:2062754 HB-7 "homeobox 7" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 281 (104.0 bits), Expect = 2.3e-29, Sum P(2) = 2.3e-29
 Identities = 65/151 (43%), Positives = 88/151 (58%)

Query:    37 NNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIE 96
             NN+RRFSDEQ+KSLE MFESE R E R K ++A ELGLQPRQVAIWFQNKRAR K+KQ+E
Sbjct:    31 NNQRRFSDEQIKSLEMMFESETRLEPRKKVQLARELGLQPRQVAIWFQNKRARWKSKQLE 90

Query:    97 REYTKLKAEFETLASSYELMRRE-HXXXXXXXXXXXXXXXXGHEDTNENSGDR------K 149
              EY  L+  ++ LAS +E +++E                    E+  + SGD+       
Sbjct:    91 TEYNILRQNYDNLASQFESLKKEKQALVSELQRLKEATQKKTQEEERQCSGDQAVVALSS 150

Query:   150 SENEITTESNER--PSQIY--VPSSDDRSRN 176
             + +E   E N R  P ++   +   DD+  +
Sbjct:   151 THHESENEENRRRKPEEVRPEMEMKDDKGHH 181

GO:0000976 "transcription regulatory region sequence-specific DNA binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA;ISS

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0009409 "response to cold" evidence=RCA

GO:0009414 "response to water deprivation" evidence=IEP;RCA

GO:0009737 "response to abscisic acid stimulus" evidence=IEP;RCA

GO:0009738 "abscisic acid mediated signaling pathway" evidence=IGI;RCA

GO:0042538 "hyperosmotic salinity response" evidence=RCA

TAIR\|locus:2079542 HB-12 "homeobox 12" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2140055 HB16 "homeobox protein 16" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2041283 HB6 "homeobox protein 6" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2202795 AtHB23 "homeobox protein 23" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2046263 HB21 "homeobox protein 21" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2168225 HB5 "homeobox protein 5" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2084228 HB-1 "homeobox 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2205075 ATHB13 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2150901 HB-3 "homeobox 3" [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:
	eugene3.00010699	hypothetical protein (196 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		223
smart00389		57	smart00389, HOX, Homeodomain	6e-12
cd00086		59	cd00086, homeodomain, Homeodomain; DNA binding dom	8e-12
pfam00046		57	pfam00046, Homeobox, Homeobox domain	9e-12
COG5576		156	COG5576, COG5576, Homeodomain-containing transcrip	1e-07
pfam02183		45	pfam02183, HALZ, Homeobox associated leucine zippe	5e-06

>gnl\|CDD\|197696 smart00389, HOX, Homeodomain	Back alignment and domain information

 Score = 58.4 bits (142), Expect = 6e-12
 Identities = 21/54 (38%), Positives = 32/54 (59%)

Query: 38 NKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
           +  F+ EQ++ LE  F+    P    +  +A +LGL  RQV +WFQN+RA+ K
Sbjct: 4  KRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 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

>gnl\|CDD\|227863 COG5576, COG5576, Homeodomain-containing transcription factor [Transcription]	Back alignment and domain information

>gnl\|CDD\|202143 pfam02183, HALZ, Homeobox associated leucine zipper	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		223
KOG0483		198	consensus Transcription factor HEX, contains HOX a	99.88
KOG0842		307	consensus Transcription factor tinman/NKX2-3, cont	99.62
KOG0488		309	consensus Transcription factor BarH and related HO	99.62
KOG0489		261	consensus Transcription factor zerknullt and relat	99.61
PF00046		57	Homeobox: Homeobox domain not present here.; Inter	99.6
KOG0843		197	consensus Transcription factor EMX1 and related HO	99.58
KOG0487		308	consensus Transcription factor Abd-B, contains HOX	99.57
KOG2251		228	consensus Homeobox transcription factor [Transcrip	99.57
KOG0485		268	consensus Transcription factor NKX-5.1/HMX1, conta	99.55
KOG0850		245	consensus Transcription factor DLX and related pro	99.54
KOG0492		246	consensus Transcription factor MSH, contains HOX d	99.51
KOG0494		332	consensus Transcription factor CHX10 and related H	99.48
KOG0484		125	consensus Transcription factor PHOX2/ARIX, contain	99.47
cd00086		59	homeodomain Homeodomain; DNA binding domains invol	99.47
smart00389		56	HOX Homeodomain. DNA-binding factors that are invo	99.47
KOG0848		317	consensus Transcription factor Caudal, contains HO	99.45
COG5576		156	Homeodomain-containing transcription factor [Trans	99.4
KOG0493		342	consensus Transcription factor Engrailed, contains	99.36
TIGR01565		58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.33
KOG4577		383	consensus Transcription factor LIM3, contains LIM	99.3
KOG0491		194	consensus Transcription factor BSH, contains HOX d	99.27
KOG3802		398	consensus Transcription factor OCT-1, contains POU	99.22
KOG0844		408	consensus Transcription factor EVX1, contains HOX	99.21
KOG0847		288	consensus Transcription factor, contains HOX domai	99.11
KOG0486		351	consensus Transcription factor PTX1, contains HOX	99.03
KOG0490		235	consensus Transcription factor, contains HOX domai	98.95
KOG0775		304	consensus Transcription factor SIX and related HOX	98.75
KOG0849		354	consensus Transcription factor PRD and related pro	98.73
KOG1168		385	consensus Transcription factor ACJ6/BRN-3, contain	98.66
PF05920		40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	98.33
PF02183		45	HALZ: Homeobox associated leucine zipper; InterPro	98.33
KOG0774		334	consensus Transcription factor PBX and related HOX	98.16
KOG2252		558	consensus CCAAT displacement protein and related h	98.11
KOG0490		235	consensus Transcription factor, contains HOX domai	97.77
KOG1146		1406	consensus Homeobox protein [General function predi	96.63
PF11569		56	Homez: Homeodomain leucine-zipper encoding, Homez;	96.46
KOG0773		342	consensus Transcription factor MEIS1 and related H	96.37
PF02183		45	HALZ: Homeobox associated leucine zipper; InterPro	95.91
KOG4005		292	consensus Transcription factor XBP-1 [Transcriptio	94.78
PRK09413		121	IS2 repressor TnpA; Reviewed	94.23
smart00340		44	HALZ homeobox associated leucin zipper.	92.65
PF04218		53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	92.0
KOG3623		1007	consensus Homeobox transcription factor SIP1 [Tran	91.86
PF06005		72	DUF904: Protein of unknown function (DUF904); Inte	91.54
PF00170		64	bZIP_1: bZIP transcription factor cAMP response el	91.17
PF06156		107	DUF972: Protein of unknown function (DUF972); Inte	91.13
PRK13169		110	DNA replication intiation control protein YabA; Re	90.29
PF10224		80	DUF2205: Predicted coiled-coil protein (DUF2205);	89.92
smart00340		44	HALZ homeobox associated leucin zipper.	89.32
PF00170		64	bZIP_1: bZIP transcription factor cAMP response el	87.85
KOG4196		135	consensus bZIP transcription factor MafK [Transcri	87.0
smart00338		65	BRLZ basic region leucin zipper.	86.43
PF06005		72	DUF904: Protein of unknown function (DUF904); Inte	85.82
KOG3119		269	consensus Basic region leucine zipper transcriptio	85.12
KOG4571		294	consensus Activating transcription factor 4 [Trans	83.89
PRK00888		105	ftsB cell division protein FtsB; Reviewed	81.6
COG4467		114	Regulator of replication initiation timing [Replic	81.21
PRK13922		276	rod shape-determining protein MreC; Provisional	80.83
TIGR00219		283	mreC rod shape-determining protein MreC. MreC (mur	80.27

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

Probab=99.88  E-value=2.4e-22  Score=171.60  Aligned_cols=103  Identities=50%  Similarity=0.721  Sum_probs=97.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 027468           35 TGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQIEREYTKLKAEFETLASSYE  114 (223)
Q Consensus        35 ~~r~R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgL~~rQVkiWFQNRRar~Krkq~~~e~~~lk~~~~~L~~~~~  114 (223)
                      ..+++.||+.+|+..||..|+.+.++.+..+..||++|||++|||+|||||||||||.++++.+|+.|+..++.|+.++.
T Consensus        50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~  129 (198)
T KOG0483|consen   50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND  129 (198)
T ss_pred             cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence            45567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC
Q 027468          115 LMRREHQLLLVQLQKLKNLLGKG  137 (223)
Q Consensus       115 ~l~~e~~~L~~e~~~L~~~~~~~  137 (223)
                      .|+.+++.|..++..++..+...
T Consensus       130 ~Lq~e~~eL~~~~~~~~~~~~~~  152 (198)
T KOG0483|consen  130 RLQSEVQELVAELSSLKREMQKS  152 (198)
T ss_pred             HHHHHHHHHHHHHhhhhhhhccC
Confidence            99999999999999888888774

>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

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

>PF00046 Homeobox: Homeobox domain not present here	Back alignment and domain information

>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]	Back alignment and domain information

>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]	Back alignment and domain information

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

>KOG0485 consensus Transcription factor NKX-5	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

>KOG0492 consensus Transcription factor MSH, 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

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

>smart00389 HOX Homeodomain	Back alignment and domain information

>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]	Back alignment and domain information

>COG5576 Homeodomain-containing transcription factor [Transcription]	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

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]	Back alignment and domain information

>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]	Back alignment and domain information

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]	Back alignment and domain information

>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]	Back alignment and domain information

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

>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

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

>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]	Back alignment and domain information

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

>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

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []	Back alignment and domain information

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

>KOG1146 consensus Homeobox protein [General function prediction only]	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

>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []	Back alignment and domain information

>KOG4005 consensus Transcription factor XBP-1 [Transcription]	Back alignment and domain information

>PRK09413 IS2 repressor TnpA; Reviewed	Back alignment and domain information

>smart00340 HALZ homeobox associated leucin zipper	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

>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]	Back alignment and domain information

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation	Back alignment and domain information

>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization

Back alignment and domain information

>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication	Back alignment and domain information

>PRK13169 DNA replication intiation control protein YabA; Reviewed	Back alignment and domain information

>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure	Back alignment and domain information

>smart00340 HALZ homeobox associated leucin zipper	Back alignment and domain information

Back alignment and domain information

>KOG4196 consensus bZIP transcription factor MafK [Transcription]	Back alignment and domain information

>smart00338 BRLZ basic region leucin zipper	Back alignment and domain information

>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation	Back alignment and domain information

>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]	Back alignment and domain information

>KOG4571 consensus Activating transcription factor 4 [Transcription]	Back alignment and domain information

>PRK00888 ftsB cell division protein FtsB; Reviewed	Back alignment and domain information

>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]	Back alignment and domain information

>PRK13922 rod shape-determining protein MreC; Provisional	Back alignment and domain information

>TIGR00219 mreC rod shape-determining protein MreC	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		223
1bw5_A		66	The Nmr Solution Structure Of The Homeodomain Of Th		2e-05
3hdd_A		60	Engrailed Homeodomain Dna Complex Length = 60		4e-04
2dmu_A		70	Solution Structure Of The Homeobox Domain Of Homeob		5e-04
1hdd_C		61	Crystal Structure Of An Engrailed Homeodomain-Dna C		5e-04

>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat Insulin Gene Enhancer Protein Isl-1, 50 Structures Length = 66

Back alignment and structure

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 34/54 (62%)
Query: 42 FSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQI 95
           +++Q+ +L   + +  RP++ MK ++ +  GL PR + +WFQNKR + K + I
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63

PyMOL of 1bw5

>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex Length = 60

Back alignment and structure

>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox Protein Goosecoid Length = 70

Back alignment and structure

>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex At 2.8 Angstroms Resolution: A Framework For Understanding Homeodomain-Dna Interactions Length = 61

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		223
1akh_A		61	Protein (mating-type protein A-1); complex (TWO DN	8e-19
2d5v_A		164	Hepatocyte nuclear factor 6; transcription factor,	2e-12
2da1_A		70	Alpha-fetoprotein enhancer binding protein; homeob	8e-11
2dn0_A		76	Zinc fingers and homeoboxes protein 3; triple home	9e-11
3nau_A		66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	2e-10
1wi3_A		71	DNA-binding protein SATB2; homeodomain, helix-turn	7e-10
2da5_A		75	Zinc fingers and homeoboxes protein 3; homeobox do	8e-10
2ecb_A		89	Zinc fingers and homeoboxes protein 1; homeobox do	3e-09
2da3_A		80	Alpha-fetoprotein enhancer binding protein; homeob	4e-09
2dmp_A		89	Zinc fingers and homeoboxes protein 2; homeobox do	6e-09
2hi3_A		73	Homeodomain-only protein; transcription; NMR {Mus	8e-09
1au7_A		146	Protein PIT-1, GHF-1; complex (DNA-binding protein	1e-08
2da2_A		70	Alpha-fetoprotein enhancer binding protein; homeob	2e-08
2cqx_A		72	LAG1 longevity assurance homolog 5; homeodomain, D	3e-08
3rkq_A		58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	3e-08
2xsd_C		164	POU domain, class 3, transcription factor 1; trans	3e-08
1nk2_P		77	Homeobox protein VND; homeodomain, DNA-binding pro	4e-08
2l9r_A		69	Homeobox protein NKX-3.1; structural genomics, nor	5e-08
1bw5_A		66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	5e-08
2djn_A		70	Homeobox protein DLX-5; structural genomics, NPPSF	1e-07
1e3o_C		160	Octamer-binding transcription factor 1; transcript	1e-07
1ftt_A		68	TTF-1 HD, thyroid transcription factor 1 homeodoma	2e-07
3l1p_A		155	POU domain, class 5, transcription factor 1; POU,	2e-07
2vi6_A		62	Homeobox protein nanog; homeodomain, DNA-binding,	2e-07
3nar_A		96	ZHX1, zinc fingers and homeoboxes protein 1; corep	2e-07
2dmq_A		80	LIM/homeobox protein LHX9; homeobox domain, three	3e-07
1ig7_A		58	Homeotic protein MSX-1; helix-turn-helix, transcri	3e-07
3a03_A		56	T-cell leukemia homeobox protein 2; homeodomain, d	7e-07
3d1n_I		151	POU domain, class 6, transcription factor 1; prote	1e-06
2ecc_A		76	Homeobox and leucine zipper protein homez; homeobo	2e-06
2kt0_A		84	Nanog, homeobox protein nanog; homeodomain, struct	2e-06
3a01_A		93	Homeodomain-containing protein; homeodomain, prote	5e-06
2e1o_A		70	Homeobox protein PRH; DNA binding protein, structu	8e-06
2dmt_A		80	Homeobox protein BARH-like 1; homeobox domain, thr	1e-05
2e19_A		64	Transcription factor 8; homeobox domain, structura	1e-05
2hdd_A		61	Protein (engrailed homeodomain Q50K); DNA binding,	1e-05
2dms_A		80	Homeobox protein OTX2; homeobox domain, three heli	2e-05
2dmu_A		70	Homeobox protein goosecoid; homeobox domain, three	6e-05
3a02_A		60	Homeobox protein aristaless; homeodomain, developm	7e-05
2cue_A		80	Paired box protein PAX6; homeobox domain, transcri	7e-05
1uhs_A		72	HOP, homeodomain only protein; structural genomics	9e-05
2k40_A		67	Homeobox expressed in ES cells 1; thermostable hom	9e-05
1yz8_P		68	Pituitary homeobox 2; DNA binding protein, transcr	1e-04
1zq3_P		68	PRD-4, homeotic bicoid protein; protein-DNA comple	2e-04
1x2m_A		64	LAG1 longevity assurance homolog 6; homeobox domai	3e-04
2da7_A		71	Zinc finger homeobox protein 1B; homeobox domain,	4e-04
1jgg_A		60	Segmentation protein EVEN-skipped; homeodomain, pr	5e-04

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A* Length = 61	Back alignment and structure

 Score = 76.1 bits (188), Expect = 8e-19
 Identities = 20/53 (37%), Positives = 28/53 (52%)

Query: 39 KRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
          K   S +    LE +F  +    S+ K  +A + G+ P QV +WF NKR RSK
Sbjct: 9  KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61

PyMOL of 1akh

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A Length = 164	Back alignment and structure

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70	Back alignment and structure

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 76	Back alignment and structure

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Length = 66	Back alignment and structure

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 71	Back alignment and structure

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75	Back alignment and structure

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 89	Back alignment and structure

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80	Back alignment and structure

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 89	Back alignment and structure

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 73	Back alignment and structure

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146	Back alignment and structure

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70	Back alignment and structure

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72	Back alignment and structure

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Length = 58	Back alignment and structure

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} Length = 164	Back alignment and structure

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A Length = 77	Back alignment and structure

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Length = 69	Back alignment and structure

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66	Back alignment and structure

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 70	Back alignment and structure

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Length = 160	Back alignment and structure

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 68	Back alignment and structure

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A Length = 155	Back alignment and structure

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Length = 62	Back alignment and structure

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens} Length = 96	Back alignment and structure

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1 Length = 58	Back alignment and structure

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Length = 56	Back alignment and structure

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Length = 151	Back alignment and structure

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 76	Back alignment and structure

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens} Length = 84	Back alignment and structure

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Length = 93	Back alignment and structure

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 70	Back alignment and structure

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 80	Back alignment and structure

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 64	Back alignment and structure

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Length = 61	Back alignment and structure

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus} Length = 80	Back alignment and structure

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70	Back alignment and structure

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A Length = 60	Back alignment and structure

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 80	Back alignment and structure

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Length = 72	Back alignment and structure

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens} Length = 67	Back alignment and structure

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P Length = 68	Back alignment and structure

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1 Length = 68	Back alignment and structure

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1 Length = 64	Back alignment and structure

>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} Length = 71	Back alignment and structure

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Length = 60	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		223
2vi6_A		62	Homeobox protein nanog; homeodomain, DNA-binding,	99.74
3a01_A		93	Homeodomain-containing protein; homeodomain, prote	99.74
2cue_A		80	Paired box protein PAX6; homeobox domain, transcri	99.74
2h1k_A		63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.74
1nk2_P		77	Homeobox protein VND; homeodomain, DNA-binding pro	99.74
2cra_A		70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.74
2dmu_A		70	Homeobox protein goosecoid; homeobox domain, three	99.73
1puf_A		77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.73
2e1o_A		70	Homeobox protein PRH; DNA binding protein, structu	99.73
2da3_A		80	Alpha-fetoprotein enhancer binding protein; homeob	99.73
2dmt_A		80	Homeobox protein BARH-like 1; homeobox domain, thr	99.73
2dmq_A		80	LIM/homeobox protein LHX9; homeobox domain, three	99.73
1ig7_A		58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.73
2da2_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.73
2kt0_A		84	Nanog, homeobox protein nanog; homeodomain, struct	99.73
1zq3_P		68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.73
2hdd_A		61	Protein (engrailed homeodomain Q50K); DNA binding,	99.73
3rkq_A		58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.73
2dms_A		80	Homeobox protein OTX2; homeobox domain, three heli	99.72
2djn_A		70	Homeobox protein DLX-5; structural genomics, NPPSF	99.72
2da1_A		70	Alpha-fetoprotein enhancer binding protein; homeob	99.72
1bw5_A		66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.72
1uhs_A		72	HOP, homeodomain only protein; structural genomics	99.72
2l7z_A		73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.72
1b8i_A		81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.71
1jgg_A		60	Segmentation protein EVEN-skipped; homeodomain, pr	99.71
3nar_A		96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.71
1ahd_P		68	Antennapedia protein mutant; DNA binding protein/D	99.71
1fjl_A		81	Paired protein; DNA-binding protein, paired BOX, t	99.71
1ftt_A		68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.71
2cqx_A		72	LAG1 longevity assurance homolog 5; homeodomain, D	99.71
2m0c_A		75	Homeobox protein aristaless-like 4; structural gen	99.71
1yz8_P		68	Pituitary homeobox 2; DNA binding protein, transcr	99.71
1wh5_A		80	ZF-HD homeobox family protein; structural genomics	99.7
2k40_A		67	Homeobox expressed in ES cells 1; thermostable hom	99.7
3a03_A		56	T-cell leukemia homeobox protein 2; homeodomain, d	99.7
2da5_A		75	Zinc fingers and homeoboxes protein 3; homeobox do	99.7
2hi3_A		73	Homeodomain-only protein; transcription; NMR {Mus	99.7
3a02_A		60	Homeobox protein aristaless; homeodomain, developm	99.7
2da4_A		80	Hypothetical protein DKFZP686K21156; homeobox doma	99.7
1akh_A		61	Protein (mating-type protein A-1); complex (TWO DN	99.69
2ecc_A		76	Homeobox and leucine zipper protein homez; homeobo	99.69
2r5y_A		88	Homeotic protein sex combs reduced; homeodomain; H	99.69
2dn0_A		76	Zinc fingers and homeoboxes protein 3; triple home	99.68
2ly9_A		74	Zinc fingers and homeoboxes protein 1; structural	99.68
1wh7_A		80	ZF-HD homeobox family protein; homeobox domain, st	99.68
1x2n_A		73	Homeobox protein pknox1; homeobox domain, structur	99.67
1b72_A		97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.67
1puf_B		73	PRE-B-cell leukemia transcription factor-1; homeod	99.67
1k61_A		60	Mating-type protein alpha-2; protein-DNA complex,	99.66
1du6_A		64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.66
2ecb_A		89	Zinc fingers and homeoboxes protein 1; homeobox do	99.65
2cuf_A		95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.65
1b72_B		87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.65
2dmn_A		83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.65
1mnm_C		87	Protein (MAT alpha-2 transcriptional repressor); t	99.65
1le8_B		83	Mating-type protein alpha-2; matalpha2, isothermal	99.64
2dmp_A		89	Zinc fingers and homeoboxes protein 2; homeobox do	99.64
1au7_A		146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.61
2l9r_A		69	Homeobox protein NKX-3.1; structural genomics, nor	99.6
2da6_A		102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.6
3nau_A		66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.6
3d1n_I		151	POU domain, class 6, transcription factor 1; prote	99.6
1e3o_C		160	Octamer-binding transcription factor 1; transcript	99.6
1wi3_A		71	DNA-binding protein SATB2; homeodomain, helix-turn	99.6
2xsd_C		164	POU domain, class 3, transcription factor 1; trans	99.59
2e19_A		64	Transcription factor 8; homeobox domain, structura	99.59
1x2m_A		64	LAG1 longevity assurance homolog 6; homeobox domai	99.59
3k2a_A		67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.57
1lfb_A		99	Liver transcription factor (LFB1); transcription r	99.56
3l1p_A		155	POU domain, class 5, transcription factor 1; POU,	99.56
2d5v_A		164	Hepatocyte nuclear factor 6; transcription factor,	99.54
2lk2_A		89	Homeobox protein TGIF1; NESG, structural genomics,	99.37
1ic8_A		194	Hepatocyte nuclear factor 1-alpha; transcription r	99.32
2da7_A		71	Zinc finger homeobox protein 1B; homeobox domain,	99.32
2h8r_A		221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.21
1mh3_A		421	Maltose binding-A1 homeodomain protein chimera; MA	99.21
2nzz_A		37	Penetratin conjugated GAS (374-394) peptide; confo	98.7
1hjb_A		87	Ccaat/enhancer binding protein beta; transcription	93.68
2ys9_A		70	Homeobox and leucine zipper protein homez; homeodo	93.64
1gu4_A		78	CAAT/enhancer binding protein beta; transcription/	93.22
1t2k_D		61	Cyclic-AMP-dependent transcription factor ATF-2; p	92.91
1ci6_A		63	Transcription factor ATF-4; BZIP; 2.60A {Homo sapi	92.7
2wt7_A		63	Proto-oncogene protein C-FOS; transcription, trans	92.03
1jnm_A		62	Proto-oncogene C-JUN; BZIP, protein-DNA complex, t	89.94
2jn6_A		97	Protein CGL2762, transposase; GFT PSI-2, protein s	89.8
1gd2_E		70	Transcription factor PAP1; basic leucine zipper, p	89.64
2yy0_A		53	C-MYC-binding protein; conserved hypothetical prot	88.6
2jee_A		81	YIIU; FTSZ, septum, coiled-coil, cell division, ce	86.98
2wt7_B		90	Transcription factor MAFB; transcription, transcri	86.24
2yy0_A		53	C-MYC-binding protein; conserved hypothetical prot	86.03
2oxj_A		34	Hybrid alpha/beta peptide based on the GCN4-P1 Se	85.95
3m48_A		33	General control protein GCN4; leucine zipper, synt	85.45
3c3g_A		33	Alpha/beta peptide with the GCN4-PLI SIDE chain S	84.88
1gd2_E		70	Transcription factor PAP1; basic leucine zipper, p	84.28
3c3f_A		34	Alpha/beta peptide with the GCN4-PLI SIDE chain S	83.71
1t2k_D		61	Cyclic-AMP-dependent transcription factor ATF-2; p	83.63
1kd8_B		36	GABH BLL, GCN4 acid base heterodimer base-D12LA16L	83.5
3m91_A		51	Proteasome-associated ATPase; coil COIL alpha heli	83.38
2dgc_A		63	Protein (GCN4); basic domain, leucine zipper, DNA	83.37
3vmx_A		48	Voltage-gated hydrogen channel 1; coiled-coil, ION	81.25
1dh3_A		55	Transcription factor CREB; protein-DNA complex, tr	80.72
2bni_A		34	General control protein GCN4; four helix bundle, a	80.23

>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

Probab=99.74  E-value=1.5e-18  Score=120.79  Aligned_cols=60  Identities=27%  Similarity=0.380  Sum_probs=53.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHhhhhhHH
Q 027468           35 TGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKTKQ   94 (223)
Q Consensus        35 ~~r~R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgL~~rQVkiWFQNRRar~Krkq   94 (223)
                      .++.|+.|+..|+..||..|..++||+...+..||..+||++.+|++||||||+++|+++
T Consensus         3 ~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~q   62 (62)
T 2vi6_A            3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ   62 (62)
T ss_dssp             -----CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGGC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhcC
Confidence            456789999999999999999999999999999999999999999999999999999864

PyMOL of 2vi6

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

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}	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

>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

>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

>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

>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

>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

>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

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>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

>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

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1	Back alignment and structure

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A	Back alignment and structure

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

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

>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

>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

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*	Back alignment and structure

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>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

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {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

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A	Back alignment and structure

>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

>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

>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

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

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}	Back alignment and structure

>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

>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

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

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1	Back alignment and structure

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>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

>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

>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

>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

>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

>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

>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

>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

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}	Back alignment and structure

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}	Back alignment and structure

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A	Back alignment and structure

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

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

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

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

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

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A	Back alignment and structure

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

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_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

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

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A	Back alignment and structure

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A	Back alignment and structure

>1hjb_A Ccaat/enhancer binding protein beta; transcription/DNA, protein-DNA complex; HET: DNA; 3.0A {Homo sapiens} SCOP: h.1.3.1	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

>1gu4_A CAAT/enhancer binding protein beta; transcription/DNA, protein-DNA complex, transcription factor, BZIP, C/EBP; 1.80A {Homo sapiens} SCOP: h.1.3.1 PDB: 1gtw_A 1gu5_A 1h88_A 1h8a_A 1io4_A 2e43_A* 2e42_A* 1h89_A 1ci6_B 1nwq_A	Back alignment and structure

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>1ci6_A Transcription factor ATF-4; BZIP; 2.60A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>2wt7_A Proto-oncogene protein C-FOS; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 1fos_E* 1a02_F* 1s9k_D	Back alignment and structure

>1jnm_A Proto-oncogene C-JUN; BZIP, protein-DNA complex, transcription/DNA complex; 2.20A {Homo sapiens} SCOP: h.1.3.1 PDB: 1fos_F 2h7h_A 1t2k_C 1a02_J* 1s9k_E 1jun_A	Back alignment and structure

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19	Back alignment and structure

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1	Back alignment and structure

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}	Back alignment and structure

>2jee_A YIIU; FTSZ, septum, coiled-coil, cell division, cell cycle, hypothetical protein; 2.8A {Escherichia coli}	Back alignment and structure

>2wt7_B Transcription factor MAFB; transcription, transcription regulation, nucleus, activator, repressor, DNA-binding, phosphoprotein, differentiation; 2.30A {Mus musculus} PDB: 2wty_A* 1k1v_A	Back alignment and structure

>2yy0_A C-MYC-binding protein; conserved hypothetical protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.40A {Homo sapiens}	Back alignment and structure

>2oxj_A Hybrid alpha/beta peptide based on the GCN4-P1 Se heptad positions B and F substituted...; helix bundle, foldamer, unknown function; HET: B3K B3D B3E B3S B3Y B3X B3A BAL; 2.00A {Synthetic} PDB: 2oxk_A*	Back alignment and structure

>3m48_A General control protein GCN4; leucine zipper, synthetic peptide, alpha helix, activa amino-acid biosynthesis, DNA-binding, nucleus; 1.45A {Synthetic} PDB: 3i1g_A 2ahp_A* 2o7h_A	Back alignment and structure

>3c3g_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-beta) backbone; helix bundle, foldamer, unknown function protein; HET: HMR B3Q B3D B3E B3L BIL B3K BAL GOL; 1.80A {Synthetic} PDB: 3heu_A* 3het_A* 3hev_A* 3hew_A* 3hey_A* 3hex_A* 3c3h_A*	Back alignment and structure

>1gd2_E Transcription factor PAP1; basic leucine zipper, protein-DNA complex, transcription/DNA complex; HET: DNA; 2.00A {Schizosaccharomyces pombe} SCOP: h.1.3.1	Back alignment and structure

>3c3f_A Alpha/beta peptide with the GCN4-PLI SIDE chain S AN (alpha-alpha-alpha-beta) backbone...; helix bundle, foldamer, unknown function, de novo protein; HET: B3K B3D B3E BIL B3L BAL; 2.00A {Synthetic} SCOP: h.1.3.1	Back alignment and structure

>1t2k_D Cyclic-AMP-dependent transcription factor ATF-2; protein DNA complex, transcription/DNA complex; 3.00A {Homo sapiens} SCOP: h.1.3.1	Back alignment and structure

>1kd8_B GABH BLL, GCN4 acid base heterodimer base-D12LA16L; coiled coil heterodimer, de novo protein; 1.90A {Synthetic} SCOP: h.1.3.1 PDB: 1kd9_B 1kdd_B	Back alignment and structure

>3m91_A Proteasome-associated ATPase; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis} PDB: 3m9h_A	Back alignment and structure

>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D	Back alignment and structure

>3vmx_A Voltage-gated hydrogen channel 1; coiled-coil, ION channel, ION transport, membrane protein; 1.45A {Mus musculus}	Back alignment and structure

>1dh3_A Transcription factor CREB; protein-DNA complex, transcription/DNA complex; HET: DNA; 3.00A {Mus musculus} SCOP: h.1.3.1	Back alignment and structure

>2bni_A General control protein GCN4; four helix bundle, antiparallel four helix bundle acyl transferase; HET: TYZ; 1.5A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 2ccn_A 1w5k_A* 2ccf_A 2cce_A 1w5j_A* 1uo2_A 1gcl_A 1uo1_A 1unv_A 1uo0_A 1unt_A 1uo5_A 1unz_A 1unx_A 1unu_A 1unw_A 1uo4_A 1uo3_A 1uny_A 1u9f_A* ...	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		223
d2e1oa1		57	a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo	3e-12
d1b72a_		88	a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo	5e-12
d1pufa_		77	a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus m	9e-12
d1k61a_		60	a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast	1e-11
d2cuea1		68	a.4.1.1 (A:7-74) Paired box protein pax6 {Human (H	3e-11
d1bw5a_		66	a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {	4e-11
d2craa1		58	a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (	5e-11
d1le8a_		53	a.4.1.1 (A:) Mating type protein A1 Homeodomain {B	8e-11
d9anta_		56	a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila	8e-11
d1jgga_		57	a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (	1e-10
d1fjla_		65	a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila	2e-10
d1p7ia_		53	a.4.1.1 (A:) Engrailed Homeodomain {Drosophila mel	3e-10
d1zq3p1		67	a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl	5e-10
d1ig7a_		58	a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu	6e-10
d1pufb_		73	a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96	7e-10
d2cqxa1		59	a.4.1.1 (A:8-66) LAG1 longevity assurance homolog	9e-10
d1yz8p1		60	a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo	9e-10
d1ftta_		68	a.4.1.1 (A:) Thyroid transcription factor 1 homeod	1e-09
d1vnda_		77	a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophi	1e-09
d1uhsa_		72	a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse	1e-09
d1x2na1		62	a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (H	2e-09
d1s7ea1		50	a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {M	3e-09
d1au7a1		58	a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Ra	4e-09
d2ecba1		76	a.4.1.1 (A:8-83) Zinc fingers and homeoboxes prote	5e-09
d1wh7a_		80	a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha	9e-09
d1x2ma1		52	a.4.1.1 (A:8-59) Lag1 longevity assurance homolog	1e-08
d2ecca1		76	a.4.1.1 (A:1-76) Homeobox-leucine zipper protein H	1e-07
d1e3oc1		57	a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (	2e-07
d1ocpa_		67	a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus mus	4e-07
d1wi3a_		71	a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom	5e-07
d1lfba_		78	a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HN	4e-05
d2cufa1		82	a.4.1.1 (A:8-89) Homeobox-containing protein 1, HM	4e-05

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Length = 57	Back information, alignment and structure


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

 Score = 57.5 bits (139), Expect = 3e-12
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 38 NKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSK 91
           + RFS++Q   LE  FE++       + R+A  L L  RQV  WFQN+RA+ +
Sbjct: 3  GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 56

PyMOL of d2e1oa1

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77	Back information, alignment and structure

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 60	Back information, alignment and structure

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Length = 68	Back information, alignment and structure

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 66	Back information, alignment and structure

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Length = 58	Back information, alignment and structure

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 53	Back information, alignment and structure

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 56	Back information, alignment and structure

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 57	Back information, alignment and structure

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65	Back information, alignment and structure

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Length = 53	Back information, alignment and structure

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 67	Back information, alignment and structure

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58	Back information, alignment and structure

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73	Back information, alignment and structure

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 59	Back information, alignment and structure

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 60	Back information, alignment and structure

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68	Back information, alignment and structure

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 77	Back information, alignment and structure

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Length = 72	Back information, alignment and structure

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Length = 62	Back information, alignment and structure

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 50	Back information, alignment and structure

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 58	Back information, alignment and structure

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]} Length = 76	Back information, alignment and structure

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80	Back information, alignment and structure

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Length = 52	Back information, alignment and structure

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

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]} Length = 57	Back information, alignment and structure

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 67	Back information, alignment and structure

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71	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

>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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		223
d2craa1		58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.8
d1pufa_		77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.8
d2e1oa1		57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.79
d9anta_		56	Antennapedia Homeodomain {Drosophila melanogaster	99.78
d1ig7a_		58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.78
d1jgga_		57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.78
d1zq3p1		67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.78
d1fjla_		65	Paired protein {Fruit fly (Drosophila melanogaster	99.77
d1p7ia_		53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.76
d2cuea1		68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.76
d1b72a_		88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.75
d1uhsa_		72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.75
d1vnda_		77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.74
d1ftta_		68	Thyroid transcription factor 1 homeodomain {Rat (R	99.74
d1yz8p1		60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.74
d1le8a_		53	Mating type protein A1 Homeodomain {Baker's yeast	99.72
d1bw5a_		66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.71
d1au7a1		58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.71
d1ocpa_		67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.71
d1wi3a_		71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.7
d1e3oc1		57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.69
d2cufa1		82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.68
d2ecba1		76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.65
d1s7ea1		50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.64
d1wh7a_		80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.63
d2ecca1		76	Homeobox-leucine zipper protein Homez {Human (Homo	99.63
d1pufb_		73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1x2ma1		52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.6
d2cqxa1		59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.57
d1k61a_		60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.57
d1lfba_		78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.55
d1x2na1		62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.5
d1hlva1		66	DNA-binding domain of centromere binding protein B	88.19
d2jn6a1		89	Uncharacterized protein Cgl2762 {Corynebacterium g	83.03

>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=99.80  E-value=2.3e-20  Score=127.91  Aligned_cols=58  Identities=24%  Similarity=0.481  Sum_probs=55.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcchhhhhhhhhHhhhhh
Q 027468           35 TGNNKRRFSDEQVKSLEFMFESEARPESRMKHRMADELGLQPRQVAIWFQNKRARSKT   92 (223)
Q Consensus        35 ~~r~R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgL~~rQVkiWFQNRRar~Kr   92 (223)
                      ++|+|++||..|+.+||..|..++||+..++.+||..|||+++||+|||||||+|+|+
T Consensus         1 Grr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           1 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            4677899999999999999999999999999999999999999999999999999885

PyMOL of d2craa1

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

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

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

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

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {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

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

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

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}	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

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

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

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

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

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

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

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {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

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

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

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

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

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

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

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}	Back information, alignment and structure

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

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}	Back information, alignment and structure