Citrus Sinensis ID: 021941

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-----
MEIKQENETKTPRRDGNNDNGTAVYSFNTHQTLDHNLQRHQQQQQARSPNPDRVTSVIGAAIAPISAGSNSKPPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVMLNPLQLPPPLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAPMNVAFGGGISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQEPAADPV
cccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccEEHHHHHHHHcccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccccEEEEEcccccccccccccccccccc
ccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccEEEEHHHHHHHHHHccccccccccccccccccccHHHHHHHHccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccEccccHHHHHHHHHHHccccEEEEEEEEcccccccccccccccccc
meikqenetktprrdgnndngtavysfnthqtLDHNLQRHQqqqqarspnpdrvTSVIGAAiapisagsnskppinviRYRECLKNHAaciggnifdgcgefmpsgdegtLEALKCAACEchrnfhrkeidGETAQLISTGrrsavmlnplqlppplpsptmmhhhhhhhqkysisrhtmspssaivapmnvafgggisesssedlsnvlhsegvlqhqppaappppppfvlskkrfRTKFTQEQKDKMMEFAEKVGwrfqkqdddQVDKFCAEVGVKRHVFKVWMHnnknntvknkqepaadpv
meikqenetktprrdgnndnGTAVYSFNTHQTLDHNLQRHQQQQQARSPNPDRVTSVIGAAiapisagsnskppiNVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVMLNPLQLPPPLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAPMNVAFGGGISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWmhnnknntvknkqepaadpv
MEIKQENETKTPRRDGNNDNGTAVYSFNTHQTLDHNLQRHqqqqqARSPNPDRVTsvigaaiapisagsnsKPPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVmlnplqlppplpsptmmhhhhhhhQKYSISRHTMSPSSAIVAPMNVAFGGGISESSSEDLSNVLHSEGVLQHQppaappppppFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFqkqdddqvdkFCAEVGVKRHVFKVWMHNNKNNTVKNKQEPAADPV
********************************************************VIGAAIAPI********PINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLI*****************************************************************************************************************FAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHN*****************
******************************************************************************RYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRR***************************************************************************************************QEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNN****************
**************DGNNDNGTAVYSFNTHQTLDH******************VTSVIGAAIAPISAGSNSKPPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVMLNPLQLPPPLPSP********************SPSSAIVAPMNVAFGGGISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK**********
********************GTAVYSFNTHQTLD***************************************PINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVMLNPLQLPPPLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAP***********************************************FRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNK***************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MEIKQENETKTPRRDGNNDNGTAVYSFNTHQTLDHNLQRHQQQQQARSPNPDRVTSVIGAAIAPISAGSNSKPPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQLISTGRRSAVMLNPLQLPPPLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAPMNVAFGGGISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKNKQEPAADPV
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 ?
Query305 2.2.26 [Sep-21-2011]
Q9SB61220 ZF-HD homeobox protein At no no 0.560 0.777 0.442 3e-41
Q9SEZ1242 Transcription factor HB29 no no 0.616 0.776 0.390 6e-32
Q9FKP8279 ZF-HD homeobox protein At no no 0.173 0.189 0.735 2e-18
>sp|Q9SB61|Y4466_ARATH ZF-HD homeobox protein At4g24660 OS=Arabidopsis thaliana GN=At4g24660 PE=1 SV=1 Back     alignment and function desciption
 Score =  169 bits (427), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 97/219 (44%), Positives = 118/219 (53%), Gaps = 48/219 (21%)

Query: 78  IRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGETAQL 137
           IRYRECLKNHA  IGG+  DGC EFMPSG++GTL+ALKCAAC CHRNFHRKE +      
Sbjct: 47  IRYRECLKNHAVNIGGHAVDGCCEFMPSGEDGTLDALKCAACGCHRNFHRKETE------ 100

Query: 138 ISTGRRSAVMLNPLQLPP-PLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAPMNVAFGG 196
            S G R+  +      PP P   P  +H                      +      +  
Sbjct: 101 -SIGGRAHRVPTYYNRPPQPHQPPGYLH----------------------LTSPAAPYRP 137

Query: 197 GISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKV 256
             +    ED SN   S G                  + KRFRTKFT EQK+KM+ FAE++
Sbjct: 138 PAASGDEEDTSNPSSSGG------------------TTKRFRTKFTAEQKEKMLAFAERL 179

Query: 257 GWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVK 295
           GWR QK DD  V++FCAE GV+R V K+WMHNNKN+  K
Sbjct: 180 GWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSLGK 218
Putative transcription factor.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9SEZ1|HB29_ARATH Transcription factor HB29 OS=Arabidopsis thaliana GN=HB29 PE=1 SV=1 Back     alignment and function description
>sp|Q9FKP8|Y5541_ARATH ZF-HD homeobox protein At5g65410 OS=Arabidopsis thaliana GN=At5g65410 PE=1 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 ?
Query305
224066213293 predicted protein [Populus trichocarpa] 0.803 0.836 0.599 2e-79
255538668289 transcription factor, putative [Ricinus 0.836 0.882 0.590 6e-79
224082868290 predicted protein [Populus trichocarpa] 0.845 0.889 0.609 1e-77
449516731320 PREDICTED: ZF-HD homeobox protein At4g24 0.724 0.690 0.661 1e-75
449470140276 PREDICTED: ZF-HD homeobox protein At4g24 0.724 0.800 0.661 2e-75
225458265316 PREDICTED: ZF-HD homeobox protein At4g24 0.714 0.689 0.589 2e-63
224134272341 predicted protein [Populus trichocarpa] 0.662 0.592 0.542 2e-58
359476692345 PREDICTED: ZF-HD homeobox protein At4g24 0.855 0.756 0.493 7e-58
297735146 410 unnamed protein product [Vitis vinifera] 0.668 0.497 0.526 7e-55
147792216250 hypothetical protein VITISV_009036 [Viti 0.714 0.872 0.524 4e-54
>gi|224066213|ref|XP_002302028.1| predicted protein [Populus trichocarpa] gi|222843754|gb|EEE81301.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  301 bits (772), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 166/277 (59%), Positives = 205/277 (74%), Gaps = 32/277 (11%)

Query: 13  RRDGNNDNGTAVYSFNTHQTLDHNLQRHQQQQQARSPNPDRVTSVIGAAIAPISAGSNSK 72
           R+DGN+ NG++V +F   QTLDH       +Q +RSPNPDR        +A IS+GSNSK
Sbjct: 28  RKDGNH-NGSSVLTFT--QTLDH------PRQPSRSPNPDR--------LAIISSGSNSK 70

Query: 73  PPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDG 132
              +  RY ECL+NHAA +GGN+FDGCGEFMP G+EG+LEALKCAAC+CHRNFHR+E+DG
Sbjct: 71  --TSNTRYLECLRNHAASVGGNVFDGCGEFMPGGEEGSLEALKCAACDCHRNFHRRELDG 128

Query: 133 ETAQLISTGRRSAVMLNPLQLPPPLPSPTMMHHHHHHHQKYSISRHTMSPSSAIVAPMNV 192
           E  Q     RRS  M++ LQL PPLPSPT++HHHHHH Q+YS+  HT   ++ +V PM+V
Sbjct: 129 EI-QFSPGSRRSTTMVHSLQLAPPLPSPTVLHHHHHH-QRYSMGLHTSPNTANMVQPMSV 186

Query: 193 AFGG--GISESSSEDLSNVLHSEGVLQHQPPAAPPPPPPFVLSKKRFRTKFTQEQKDKMM 250
           AFGG  G +ESSSE+L+           Q  A   PPPP+V+SKKR RTKFTQEQKDKMM
Sbjct: 187 AFGGTSGGTESSSEELNPF---------QSNAEGAPPPPYVMSKKRHRTKFTQEQKDKMM 237

Query: 251 EFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMH 287
           EFAEKVGWR  KQD+++V++FCAEVGV+R VFKVWMH
Sbjct: 238 EFAEKVGWRINKQDEEEVERFCAEVGVRRQVFKVWMH 274

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|255538668|ref|XP_002510399.1| transcription factor, putative [Ricinus communis] gi|223551100|gb|EEF52586.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224082868|ref|XP_002306871.1| predicted protein [Populus trichocarpa] gi|222856320|gb|EEE93867.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449516731|ref|XP_004165400.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|449470140|ref|XP_004152776.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|225458265|ref|XP_002281371.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|224134272|ref|XP_002327798.1| predicted protein [Populus trichocarpa] gi|222836883|gb|EEE75276.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|359476692|ref|XP_002266577.2| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|297735146|emb|CBI17508.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|147792216|emb|CAN72985.1| hypothetical protein VITISV_009036 [Vitis vinifera] 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 ?
Query305
TAIR|locus:2025121309 HB33 "AT1G75240" [Arabidopsis 0.452 0.446 0.433 3.3e-55
TAIR|locus:2062141262 HB24 "AT2G18350" [Arabidopsis 0.426 0.496 0.397 1.4e-44
TAIR|locus:2065304310 HB21 "homeobox protein 21" [Ar 0.213 0.209 0.651 1.1e-42
TAIR|locus:2012602312 HB31 "AT1G14440" [Arabidopsis 0.193 0.189 0.711 2.8e-42
TAIR|locus:2121989220 HB22 "AT4G24660" [Arabidopsis 0.206 0.286 0.692 3.6e-40
TAIR|locus:2077957249 HB28 "homeobox protein 28" [Ar 0.177 0.216 0.703 4e-37
TAIR|locus:2168240279 HB25 "AT5G65410" [Arabidopsis 0.170 0.186 0.75 9.2e-36
TAIR|locus:2095157312 HB34 "AT3G28920" [Arabidopsis 0.196 0.192 0.612 2.4e-35
TAIR|locus:2150871271 HB30 "AT5G15210" [Arabidopsis 0.193 0.217 0.593 1e-34
TAIR|locus:2167052334 HB23 "AT5G39760" [Arabidopsis 0.4 0.365 0.377 3.8e-34
TAIR|locus:2025121 HB33 "AT1G75240" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 304 (112.1 bits), Expect = 3.3e-55, Sum P(2) = 3.3e-55
 Identities = 62/143 (43%), Positives = 81/143 (56%)

Query:     1 MEIKQENETKTPRRDGNNDNGTAVYSFNTHQTLDHNLQRHXXXXXARSPNPDRVTXXXXX 60
             M+++     +  R D  N+NG  V S      +D N   +       S N   +      
Sbjct:     1 MDMRSHEMIERRREDNGNNNGGVVISNIISTNIDDNCNGNNNNTRV-SCNSQTLDHHQSK 59

Query:    61 XXXXXXXXXXXKPPINVIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACE 120
                        KP    +RYRECLKNHAA +GG++ DGCGEFMPSG+EGT+EAL+CAAC+
Sbjct:    60 SPSSFSISAAAKP---TVRYRECLKNHAASVGGSVHDGCGEFMPSGEEGTIEALRCAACD 116

Query:   121 CHRNFHRKEIDGE-TAQLISTGR 142
             CHRNFHRKE+DG  ++ LIS  R
Sbjct:   117 CHRNFHRKEMDGVGSSDLISHHR 139
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;IDA
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0003677 "DNA binding" evidence=IPI
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA
GO:0009737 "response to abscisic acid stimulus" evidence=IMP
GO:0010103 "stomatal complex morphogenesis" evidence=RCA
TAIR|locus:2062141 HB24 "AT2G18350" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2065304 HB21 "homeobox protein 21" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2012602 HB31 "AT1G14440" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2121989 HB22 "AT4G24660" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2077957 HB28 "homeobox protein 28" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2168240 HB25 "AT5G65410" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2095157 HB34 "AT3G28920" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2150871 HB30 "AT5G15210" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2167052 HB23 "AT5G39760" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query305
pfam0477060 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation 1e-33
TIGR0156558 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD cla 2e-27
TIGR0156653 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cy 2e-25
>gnl|CDD|218256 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation region Back     alignment and domain information 
 Score =  117 bits (294), Expect = 1e-33
 Identities = 43/58 (74%), Positives = 50/58 (86%)

Query: 77  VIRYRECLKNHAACIGGNIFDGCGEFMPSGDEGTLEALKCAACECHRNFHRKEIDGET 134
            +RYRECLKNHAA IGG+  DGCGEFMPSG+EGT ++LKCAAC CHRNFHR+E +GE 
Sbjct: 3   GVRYRECLKNHAASIGGHAVDGCGEFMPSGEEGTPDSLKCAACGCHRNFHRREPEGEV 60

This family of proteins has are plant transcription factors, and have been named ZF-HD for zinc finger homeodomain proteins, on the basis of similarity to proteins of known structure. This region is thought to be involved in the formation of homo and heterodimers, and may form a zinc finger. Length = 60
>gnl|CDD|130628 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD class Back     alignment and domain information
>gnl|CDD|130629 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cys/His-rich dimerization domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 305
PF0477060 ZF-HD_dimer: ZF-HD protein dimerisation region; In 100.0
TIGR0156653 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich d 100.0
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.94
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.2
KOG4577 383 consensus Transcription factor LIM3, contains LIM 99.12
KOG0494 332 consensus Transcription factor CHX10 and related H 99.11
KOG2251 228 consensus Homeobox transcription factor [Transcrip 99.05
KOG0843197 consensus Transcription factor EMX1 and related HO 99.03
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.01
KOG0493342 consensus Transcription factor Engrailed, contains 98.9
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 98.86
cd0008659 homeodomain Homeodomain; DNA binding domains invol 98.82
KOG0844 408 consensus Transcription factor EVX1, contains HOX 98.62
KOG3802398 consensus Transcription factor OCT-1, contains POU 98.59
KOG0490 235 consensus Transcription factor, contains HOX domai 98.54
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 98.34
KOG0488309 consensus Transcription factor BarH and related HO 98.3
KOG0489261 consensus Transcription factor zerknullt and relat 98.27
KOG0850245 consensus Transcription factor DLX and related pro 98.25
COG5576156 Homeodomain-containing transcription factor [Trans 98.23
KOG0492246 consensus Transcription factor MSH, contains HOX d 98.16
KOG0849 354 consensus Transcription factor PRD and related pro 98.03
KOG0486 351 consensus Transcription factor PTX1, contains HOX 98.02
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 98.02
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 97.87
KOG0490235 consensus Transcription factor, contains HOX domai 97.85
KOG0483198 consensus Transcription factor HEX, contains HOX a 97.67
KOG1146 1406 consensus Homeobox protein [General function predi 97.61
KOG0847288 consensus Transcription factor, contains HOX domai 97.46
KOG2252558 consensus CCAAT displacement protein and related h 97.33
KOG0487308 consensus Transcription factor Abd-B, contains HOX 97.13
KOG0848317 consensus Transcription factor Caudal, contains HO 97.06
KOG0491194 consensus Transcription factor BSH, contains HOX d 97.05
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 94.93
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 94.4
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 89.53
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 88.65
COG2963116 Transposase and inactivated derivatives [DNA repli 81.56
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 80.36
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors Back     alignment and domain information 
Probab=100.00  E-value=5.6e-38  Score=235.82  Aligned_cols=57  Identities=79%  Similarity=1.492  Sum_probs=54.4

Q ss_pred             ceEeehhhhhhhhcccCCceeccccccccC-CCCCCcccccccccccccccccccccC
Q 021941           76 NVIRYRECLKNHAACIGGNIFDGCGEFMPS-GDEGTLEALKCAACECHRNFHRKEIDG  132 (305)
Q Consensus        76 ~~v~Y~EClkNHAa~~Gg~a~DGCgEFmp~-~~~gt~~al~CaACgCHRnFHrke~~~  132 (305)
                      ..|+||||||||||+||||+||||+||||+ +++|++++|+||||||||||||||+++
T Consensus         2 ~~v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~~~al~CaACgCHRnFHRre~~~   59 (60)
T PF04770_consen    2 KVVRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGTPEALKCAACGCHRNFHRREVEG   59 (60)
T ss_pred             CceeHHHHHhhHhHhhCCcccccccccccCCCCCCCcccceecccCcchhcccCCcCC
Confidence            368999999999999999999999999999 889999999999999999999999865

HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain Back     alignment and domain information
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription] Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>smart00389 HOX Homeodomain Back     alignment and domain information
>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
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0485 consensus Transcription factor NKX-5 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
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] Back     alignment and domain information
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>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
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>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
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs) Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query305
1wh7_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 5e-16
1wh5_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 6e-13
>pdb|1WH7|A Chain A, Solution Structure Of Homeobox Domain Of Arabidopsis Thaliana Hypothetical Protein F22k18.140 Length = 80 Back     alignment and structure 
Iteration: 1

 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 35/60 (58%), Positives = 43/60 (71%)
Query: 233 SKKRFRTKFTQEQKDKMMEFAEKVGWRFXXXXXXXXXXFCAEVGVKRHVFKVWMHNNKNN 292
           + KRFRTKFT EQK+KM+ FAE++GWR           FCAE GV+R V K+WMHNNKN+
Sbjct: 16  TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 75
>pdb|1WH5|A Chain A, Solution Structure Of Homeobox Domain Of Arabidopsisthaliana Zinc Finger Homeobox Family Protein Length = 80 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 ?
Query305
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 3e-37
1wh5_A80 ZF-HD homeobox family protein; structural genomics 2e-36
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-05
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 6e-04
>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 Length = 80 Back     alignment and structure
 Score =  126 bits (318), Expect = 3e-37
 Identities = 41/76 (53%), Positives = 54/76 (71%)

Query: 221 PAAPPPPPPFVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRH 280
            ++   P     + KRFRTKFT EQK+KM+ FAE++GWR QK DD  V++FCAE GV+R 
Sbjct: 4   GSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQ 63

Query: 281 VFKVWMHNNKNNTVKN 296
           V K+WMHNNKN+   +
Sbjct: 64  VLKIWMHNNKNSGPSS 79
>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 Length = 80 Back     alignment and structure
>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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query305
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.84
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.81
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.55
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.54
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.51
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.5
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.44
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.43
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.42
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.41
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.41
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.39
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.38
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.38
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.36
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.35
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.34
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.34
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.34
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.33
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.32
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.31
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.31
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.31
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.3
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.29
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.29
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.29
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.28
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.27
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.27
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.27
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.26
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.26
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.26
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.26
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.25
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.25
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.24
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.23
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.22
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.2
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.2
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.2
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.19
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.19
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.18
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.18
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.16
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.14
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.14
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.13
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.13
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.1
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.07
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.07
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.07
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.06
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.05
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.05
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.05
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.03
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.03
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 98.99
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 98.98
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 98.97
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 98.9
2e19_A64 Transcription factor 8; homeobox domain, structura 98.83
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 98.76
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 98.66
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 98.6
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 98.58
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 98.57
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 98.56
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 98.47
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 98.35
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 97.64
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 95.35
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 93.3
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 91.94
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 90.35
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 89.07
2ofy_A86 Putative XRE-family transcriptional regulator; tra 87.69
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 87.13
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 86.7
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 86.67
>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
Probab=99.84  E-value=1.5e-21  Score=150.75  Aligned_cols=67  Identities=60%  Similarity=1.024  Sum_probs=63.5

Q ss_pred             CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941          230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN  296 (305)
Q Consensus       230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK  296 (305)
                      ....+||.||.||.+|++.|++|++++||+.+++|..++++||.+|||++.+|||||||+|+++++.
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~s   79 (80)
T 1wh7_A           13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCCC
Confidence            4456899999999999999999999999999999999999999999999999999999999999863
>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
>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
>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
>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
>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
>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
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Back     alignment and structure
>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
>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
>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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, 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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} Back     alignment and structure
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A Back     alignment and structure
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Back     alignment and structure
>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
>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
>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
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B Back     alignment and structure
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>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
>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
>2hi3_A Homeodomain-only protein; transcription; 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
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>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
>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
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens} Back     alignment and structure
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens} Back     alignment and structure
>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
>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
>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
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens} Back     alignment and structure
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A Back     alignment and structure
>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster} Back     alignment and structure
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>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
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3 Back     alignment and structure
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2 Back     alignment and structure
>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C Back     alignment and structure

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 305
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 1e-12
d1b72a_88 a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo 2e-05
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 3e-04
d1ftta_68 a.4.1.1 (A:) Thyroid transcription factor 1 homeod 8e-04
d1pufb_73 a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 96 0.003
d1ig7a_58 a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculu 0.003
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 0.004
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 80 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 60.4 bits (146), Expect = 1e-12
 Identities = 40/60 (66%), Positives = 50/60 (83%)

Query: 233 SKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNN 292
           + KRFRTKFT EQK+KM+ FAE++GWR QK DD  V++FCAE GV+R V K+WMHNNKN+
Sbjct: 16  TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 75
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Length = 88 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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 68 Back     information, alignment and structure
>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]} Length = 73 Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Length = 58 Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 65 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 ?
Query305
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.86
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.5
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.48
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.46
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.44
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.42
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.42
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.41
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.4
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.4
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.38
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.38
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.38
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.38
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.37
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.35
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.34
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.31
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.31
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.27
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.24
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.19
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.18
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.16
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.14
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.06
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.0
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 98.92
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 98.78
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 98.77
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 98.76
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 98.68
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 88.05
>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.86  E-value=1.4e-22  Score=155.10  Aligned_cols=67  Identities=60%  Similarity=1.024  Sum_probs=63.0

Q ss_pred             CCCCCCccCcCCCHHHHHHHHHHHHHhCCccCCCCHHHHHHHHHHhCCCCceEEEecccccccCCCC
Q 021941          230 FVLSKKRFRTKFTQEQKDKMMEFAEKVGWRFQKQDDDQVDKFCAEVGVKRHVFKVWMHNNKNNTVKN  296 (305)
Q Consensus       230 ~~~~kKR~RTkFT~EQkekM~~fAEklGWRiqk~de~~ve~fC~eiGV~r~V~KVWmhNnK~~~~kK  296 (305)
                      ....+||.||.||.+|++.|++|+|+++|+++++|++++++||.+|||+++||||||||+|++.++.
T Consensus        13 ~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~~   79 (80)
T d1wh7a_          13 SGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCCC
Confidence            3456789999999999999999999999999999999999999999999999999999999998764
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU 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
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {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
>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
>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
>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {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
>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic} Back     information, alignment and structure