Citrus Sinensis ID: 048824

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-------21
MDLSLVPYKHQRPHPQQEPNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQLLLQPKRLLLFKDPTKLVGAVDRYDEYDRRSETPEREEVNLNVCPPGNVGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESASQSPTEAAPPAAA
cccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHcccccEEEEEccccccccccccccccccccccccccccc
ccccccccccccccccccccEEEEHHHHHHHHHHccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccEccccHHHHHHHHHHHccccEEEEEEEEccccccccccccccccccccccccccc
mdlslvpykhqrphpqqepniinYKECMKNHAasigghandgccefmpraddsltcaacgchrnfhrreVRGQlllqpkrlllfkdptklvgavdrydeydrrsetpereevnlnvcppgnvgpatgkskrqrTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHnnknashrrkdesasqspteaappaaa
mdlslvpykhqrphpqqepNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQlllqpkrlllfkdptklvgavdrydeydrrsetpereevnlnvcppgnvgpatgkskrqrtkftqeqKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNnknashrrkdesasqspteaappaaa
MDLSLVPYKHQRPHPQQEPNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQlllqpkrlllFKDPTKLVGAVDRYDEYDRRSETPEREEVNLNVCPPGNVGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESASQSPTEAAPPAAA
********************IINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQLLLQPKRLLLFKDPTKLVGAVDRYD**********************************************LEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMH***************************
***********************YKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQ**LQP************************************************************EQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHN**************************
MDLSLVPYKHQRPHPQQEPNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQLLLQPKRLLLFKDPTKLVGAVDRYD*************VNLNVCPPGNVG**************QEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK************************
****LVPYKHQRPHPQQEPNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQLLLQPKRLLLFKDPTKLVGAV**************************************RTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MDLSLVPYKHQRPHPQQEPNIINYKECMKNHAASIGGHANDGCCEFMPRADDSLTCAACGCHRNFHRREVRGQLLLQPKRLLLFKDPTKLVGAVDRYDEYDRRSETPEREEVNLNVCPPGNVGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKDESASQSPTEAAPPAAA
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 ?
Query209 2.2.26 [Sep-21-2011]
Q9SB61220 ZF-HD homeobox protein At yes no 0.712 0.677 0.462 8e-40
Q9FKP8279 ZF-HD homeobox protein At no no 0.751 0.562 0.424 2e-32
Q9SEZ1242 Transcription factor HB29 no no 0.765 0.661 0.436 3e-31
>sp|Q9SB61|Y4466_ARATH ZF-HD homeobox protein At4g24660 OS=Arabidopsis thaliana GN=At4g24660 PE=1 SV=1 Back     alignment and function desciption
 Score =  163 bits (413), Expect = 8e-40,   Method: Compositional matrix adjust.
 Identities = 86/186 (46%), Positives = 106/186 (56%), Gaps = 37/186 (19%)

Query: 22  INYKECMKNHAASIGGHANDGCCEFMPRADD----SLTCAACGCHRNFHRREVRGQLLLQ 77
           I Y+EC+KNHA +IGGHA DGCCEFMP  +D    +L CAACGCHRNFHR+E        
Sbjct: 47  IRYRECLKNHAVNIGGHAVDGCCEFMPSGEDGTLDALKCAACGCHRNFHRKETE------ 100

Query: 78  PKRLLLFKDPTKLVGAVDRYDEYDRRSETPEREEVNLNVCP----------------PGN 121
                       + G   R   Y  R   P +    L++                    N
Sbjct: 101 -----------SIGGRAHRVPTYYNRPPQPHQPPGYLHLTSPAAPYRPPAASGDEEDTSN 149

Query: 122 VGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWM 181
              + G +KR RTKFT EQK+KML FAER+GWR+Q+ DDVA+ QFC E GV+R VLK+WM
Sbjct: 150 PSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWM 209

Query: 182 HNNKNA 187
           HNNKN+
Sbjct: 210 HNNKNS 215
Putative transcription factor.
Arabidopsis thaliana (taxid: 3702)
>sp|Q9FKP8|Y5541_ARATH ZF-HD homeobox protein At5g65410 OS=Arabidopsis thaliana GN=At5g65410 PE=1 SV=1 Back     alignment and function description
>sp|Q9SEZ1|HB29_ARATH Transcription factor HB29 OS=Arabidopsis thaliana GN=HB29 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 ?
Query209
255588035245 transcription factor, putative [Ricinus 0.894 0.763 0.556 9e-55
225460528275 PREDICTED: ZF-HD homeobox protein At4g24 0.885 0.672 0.460 6e-48
147790096243 hypothetical protein VITISV_004128 [Viti 0.775 0.666 0.514 5e-47
224145148171 predicted protein [Populus trichocarpa] 0.746 0.912 0.576 2e-46
224135979219 predicted protein [Populus trichocarpa] 0.885 0.844 0.526 3e-45
296081010266 unnamed protein product [Vitis vinifera] 0.712 0.560 0.497 1e-41
164562221211 zinc finger-homeodomain protein 3, parti 0.851 0.843 0.460 1e-40
312282963227 unnamed protein product [Thellungiella h 0.708 0.651 0.460 3e-38
224119848177 predicted protein [Populus trichocarpa] 0.755 0.892 0.474 4e-38
297799540214 ATHB22/MEE68 [Arabidopsis lyrata subsp. 0.712 0.696 0.452 4e-38
>gi|255588035|ref|XP_002534484.1| transcription factor, putative [Ricinus communis] gi|223525213|gb|EEF27897.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  218 bits (556), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 128/230 (55%), Positives = 150/230 (65%), Gaps = 43/230 (18%)

Query: 1   MDLSLVPYKHQR------------PHP-QQEPNIINYKECMKNHAASIGGHANDGCCEFM 47
           MDL+LVP++ QR            P+P     N++ YKECMKNHAASIGGHANDGC EFM
Sbjct: 1   MDLTLVPFQQQREDGDGKHKNRHNPNPISAYFNLVKYKECMKNHAASIGGHANDGCGEFM 60

Query: 48  PRADDS-LTCAACGCHRNFHRRE-------VRGQLLLQPKRLLLFKDPTKLVGAVDRYDE 99
           P ADD+ LTCAACGCHRNFHRRE        R    L  + LLL   P     +V    +
Sbjct: 61  PCADDNNLTCAACGCHRNFHRREGTSAASSARQHHTLHFEHLLLSPPPLAAAKSVTVSKK 120

Query: 100 Y----------------DRRSETPEREEVNLNVCPPGNVGPATGKSKRQRTKFTQEQKDK 143
           +                DRRSETPER EVN      G +G +  K+KR RTKFTQEQKD+
Sbjct: 121 HLITSHDHSDDPEDDDHDRRSETPERGEVN----HVGGLG-SRAKNKRFRTKFTQEQKDR 175

Query: 144 MLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRRKD 193
           MLEFAE+IGWR+ + DD+ALNQFC+EVGVKR+VLKVWMHNNKNA HRR+D
Sbjct: 176 MLEFAEKIGWRINKNDDMALNQFCDEVGVKRNVLKVWMHNNKNA-HRRRD 224

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225460528|ref|XP_002276580.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|147790096|emb|CAN64849.1| hypothetical protein VITISV_004128 [Vitis vinifera] Back     alignment and taxonomy information
>gi|224145148|ref|XP_002325543.1| predicted protein [Populus trichocarpa] gi|222862418|gb|EEE99924.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224135979|ref|XP_002327351.1| predicted protein [Populus trichocarpa] gi|222835721|gb|EEE74156.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|296081010|emb|CBI18514.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|164562221|gb|ABY61025.1| zinc finger-homeodomain protein 3, partial [Saruma henryi] Back     alignment and taxonomy information
>gi|312282963|dbj|BAJ34347.1| unnamed protein product [Thellungiella halophila] Back     alignment and taxonomy information
>gi|224119848|ref|XP_002331077.1| predicted protein [Populus trichocarpa] gi|222872805|gb|EEF09936.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|297799540|ref|XP_002867654.1| ATHB22/MEE68 [Arabidopsis lyrata subsp. lyrata] gi|297313490|gb|EFH43913.1| ATHB22/MEE68 [Arabidopsis lyrata subsp. lyrata] 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 ?
Query209
TAIR|locus:2012602312 HB31 "AT1G14440" [Arabidopsis 0.277 0.185 0.672 3.6e-40
TAIR|locus:2065304310 HB21 "homeobox protein 21" [Ar 0.373 0.251 0.531 4.6e-40
TAIR|locus:2121989220 HB22 "AT4G24660" [Arabidopsis 0.760 0.722 0.494 2.9e-39
TAIR|locus:2167052334 HB23 "AT5G39760" [Arabidopsis 0.311 0.194 0.6 8.3e-39
TAIR|locus:2095157312 HB34 "AT3G28920" [Arabidopsis 0.358 0.240 0.539 7.3e-38
TAIR|locus:2025121309 HB33 "AT1G75240" [Arabidopsis 0.291 0.197 0.606 4e-37
TAIR|locus:2062141262 HB24 "AT2G18350" [Arabidopsis 0.301 0.240 0.625 4e-37
TAIR|locus:2168240279 HB25 "AT5G65410" [Arabidopsis 0.287 0.215 0.666 5.7e-36
TAIR|locus:2026734242 ZFHD1 "AT1G69600" [Arabidopsis 0.267 0.231 0.625 3.4e-34
TAIR|locus:2077957249 HB28 "homeobox protein 28" [Ar 0.937 0.787 0.392 1.2e-33
TAIR|locus:2012602 HB31 "AT1G14440" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 229 (85.7 bits), Expect = 3.6e-40, Sum P(2) = 3.6e-40
 Identities = 39/58 (67%), Positives = 49/58 (84%)

Query:   128 KSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNK 185
             + KR RTKFT EQK+KML FAE++GW++QRQ+D  + +FC E+GVKR VLKVWMHNNK
Sbjct:   217 QKKRFRTKFTPEQKEKMLSFAEKVGWKIQRQEDCVVQRFCEEIGVKRRVLKVWMHNNK 274
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0005634 "nucleus" evidence=ISM
TAIR|locus:2065304 HB21 "homeobox protein 21" [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:2167052 HB23 "AT5G39760" [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:2025121 HB33 "AT1G75240" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2062141 HB24 "AT2G18350" [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:2026734 ZFHD1 "AT1G69600" [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

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 ?
Query209
pfam0477060 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation 2e-29
TIGR0156653 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cy 2e-23
TIGR0156558 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD cla 6e-22
>gnl|CDD|218256 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation region Back     alignment and domain information 
 Score =  103 bits (258), Expect = 2e-29
 Identities = 38/51 (74%), Positives = 41/51 (80%), Gaps = 4/51 (7%)

Query: 24 YKECMKNHAASIGGHANDGCCEFMPRAD----DSLTCAACGCHRNFHRREV 70
          Y+EC+KNHAASIGGHA DGC EFMP  +    DSL CAACGCHRNFHRRE 
Sbjct: 6  YRECLKNHAASIGGHAVDGCGEFMPSGEEGTPDSLKCAACGCHRNFHRREP 56

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|130629 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cys/His-rich dimerization domain Back     alignment and domain information
>gnl|CDD|130628 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD class Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 209
TIGR0156653 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich d 100.0
PF0477060 ZF-HD_dimer: ZF-HD protein dimerisation region; In 100.0
TIGR0156558 homeo_ZF_HD homeobox domain, ZF-HD class. This mod 99.93
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.51
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.49
KOG2251 228 consensus Homeobox transcription factor [Transcrip 99.48
KOG3802398 consensus Transcription factor OCT-1, contains POU 99.46
KOG0843197 consensus Transcription factor EMX1 and related HO 99.44
KOG0494 332 consensus Transcription factor CHX10 and related H 99.43
KOG4577 383 consensus Transcription factor LIM3, contains LIM 99.41
KOG0493342 consensus Transcription factor Engrailed, contains 99.38
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.3
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.27
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.26
KOG0488309 consensus Transcription factor BarH and related HO 99.23
KOG0489261 consensus Transcription factor zerknullt and relat 99.21
KOG0844 408 consensus Transcription factor EVX1, contains HOX 99.19
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.16
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.11
KOG0490235 consensus Transcription factor, contains HOX domai 99.11
KOG0850245 consensus Transcription factor DLX and related pro 99.05
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 99.04
KOG0486 351 consensus Transcription factor PTX1, contains HOX 99.0
COG5576156 Homeodomain-containing transcription factor [Trans 98.87
KOG0849 354 consensus Transcription factor PRD and related pro 98.82
KOG0848317 consensus Transcription factor Caudal, contains HO 98.74
KOG0487308 consensus Transcription factor Abd-B, contains HOX 98.73
KOG0483198 consensus Transcription factor HEX, contains HOX a 98.69
KOG0847288 consensus Transcription factor, contains HOX domai 98.52
KOG0491194 consensus Transcription factor BSH, contains HOX d 98.48
KOG1146 1406 consensus Homeobox protein [General function predi 98.26
KOG0490235 consensus Transcription factor, contains HOX domai 98.2
KOG2252558 consensus CCAAT displacement protein and related h 98.13
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 96.75
KOG0774334 consensus Transcription factor PBX and related HOX 96.37
KOG0775304 consensus Transcription factor SIX and related HOX 96.0
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 95.87
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 95.56
KOG0773342 consensus Transcription factor MEIS1 and related H 94.73
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 93.66
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 90.92
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 90.22
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 89.6
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 87.47
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 85.18
PRK09413121 IS2 repressor TnpA; Reviewed 84.74
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 84.66
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 84.61
COG2963116 Transposase and inactivated derivatives [DNA repli 84.24
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 81.77
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 80.6
PRK06759154 RNA polymerase factor sigma-70; Validated 80.42
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain Back     alignment and domain information 
Probab=100.00  E-value=1.2e-36  Score=212.60  Aligned_cols=48  Identities=79%  Similarity=1.448  Sum_probs=44.6

Q ss_pred             eehHhhhhhhhhcCCccccccccccc-CCCC----cccccccccccccccccc
Q 048824           23 NYKECMKNHAASIGGHANDGCCEFMP-RADD----SLTCAACGCHRNFHRREV   70 (209)
Q Consensus        23 ~Y~eC~kNhaa~~Gg~~~DGC~Efm~-~~~~----~l~CaaCgCHRnFHr~e~   70 (209)
                      +|+||||||||+|||||||||||||| ++++    +|+||||||||||||||+
T Consensus         1 ~Y~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~~~al~CaACgCHRnFHRre~   53 (53)
T TIGR01566         1 LYKECLKNHAASIGGHALDGCGEFMPSSGEEGDPESLTCAACGCHRNFHRKEP   53 (53)
T ss_pred             CHHHHHHhhHHHhCCcccccccccccCCCCCCCCcceeeeecCcccccccCCC
Confidence            69999999999999999999999999 4543    999999999999999984

This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
>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
>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
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [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
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [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
>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
>KOG0844 consensus Transcription factor EVX1, 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
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [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
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription] Back     alignment and domain information
>KOG0847 consensus Transcription factor, 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
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>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
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] 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
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition Back     alignment and domain information
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription] Back     alignment and domain information
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella Back     alignment and domain information
>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
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif Back     alignment and domain information
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms Back     alignment and domain information
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK09413 IS2 repressor TnpA; Reviewed Back     alignment and domain information
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query209
1wh7_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 3e-21
1wh5_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 2e-18
>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 = 98.2 bits (243), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 42/59 (71%), Positives = 51/59 (86%)
Query: 129 SKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNA 187
           +KR RTKFT EQK+KML FAER+GWR+Q+ DDVA+ QFC E GV+R VLK+WMHNNKN+
Sbjct: 17  TKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 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 ?
Query209
1wh5_A80 ZF-HD homeobox family protein; structural genomics 4e-33
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 9e-33
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 1e-05
>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
 Score =  113 bits (283), Expect = 4e-33
 Identities = 40/70 (57%), Positives = 49/70 (70%)

Query: 118 PPGNVGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVL 177
              +     G  KR RTKFT EQK++ML  AERIGWR+QRQDD  + +FC E GV R VL
Sbjct: 6   SGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVL 65

Query: 178 KVWMHNNKNA 187
           KVW+HNNK++
Sbjct: 66  KVWLHNNKHS 75
>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
>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 ?
Query209
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.89
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.88
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.76
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.73
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.71
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.7
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.7
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.69
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.69
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.68
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.68
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.68
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.67
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.66
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.65
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.65
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.65
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.64
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.63
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.63
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.62
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.62
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.62
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.62
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.61
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.61
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.61
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.61
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.61
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.6
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.59
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.59
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.59
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.58
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.58
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.58
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.58
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.58
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.57
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.57
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.57
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.57
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.57
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.57
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.57
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.54
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.54
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.53
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.53
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.52
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.52
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.51
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.51
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.51
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.51
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.5
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.5
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.49
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.48
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.48
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.47
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.46
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.45
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.44
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.41
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.39
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.39
2e19_A64 Transcription factor 8; homeobox domain, structura 99.37
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.28
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.28
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.27
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.2
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.17
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.13
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.06
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 98.95
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 98.72
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 97.67
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 94.99
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 93.89
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 93.3
2ofy_A86 Putative XRE-family transcriptional regulator; tra 91.31
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 91.28
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 91.18
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 90.64
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 89.8
1iuf_A144 Centromere ABP1 protein; riken structural genomics 87.47
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 86.59
3c57_A95 Two component transcriptional regulatory protein; 84.56
1u78_A141 TC3 transposase, transposable element TC3 transpos 84.34
2qko_A 215 Possible transcriptional regulator, TETR family P; 84.16
3bdn_A 236 Lambda repressor; repressor, allostery; HET: DNA; 84.07
2ao9_A155 Phage protein; structural genomics, nine-fold NCS. 84.01
3gzi_A 218 Transcriptional regulator, TETR family; TETR famil 83.85
3cwr_A 208 Transcriptional regulator, TETR family; YP_425770. 83.79
2k27_A159 Paired box protein PAX-8; paired domain, solution 83.1
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 82.26
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 82.23
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type dom 82.01
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 81.75
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 81.4
3bni_A 229 Putative TETR-family transcriptional regulator; st 81.33
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 80.93
3kz9_A 206 SMCR; transcriptional regulator, quorum S DNA-bind 80.32
3kz3_A80 Repressor protein CI; five helix bundle, DNA-bindi 80.25
>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=99.89  E-value=6.4e-24  Score=156.33  Aligned_cols=66  Identities=65%  Similarity=1.134  Sum_probs=63.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824          126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR  191 (209)
Q Consensus       126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~  191 (209)
                      ..++||.||.||.+|+++|++|++++||+.+|||..++++||.+|||++.+|||||||+|+|+++.
T Consensus        14 ~~~~rR~Rt~ft~~Ql~~Le~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~s   79 (80)
T 1wh7_A           14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCCC
Confidence            456899999999999999999999999999999999999999999999999999999999999873
>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
>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
>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
>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
>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
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus} Back     alignment and structure
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} 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
>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
>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
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} 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
>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
>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
>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
>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
>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
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B* Back     alignment and structure
>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
>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
>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
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus} 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
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1 Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A 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
>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
>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
>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
>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
>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
>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
>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
>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
>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A Back     alignment and structure
>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster} Back     alignment and structure
>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
>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
>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
>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
>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri} Back     alignment and structure
>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7 Back     alignment and structure
>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A Back     alignment and structure
>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A Back     alignment and structure
>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2 Back     alignment and structure
>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP} Back     alignment and structure
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Back     alignment and structure
>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17 Back     alignment and structure
>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4} Back     alignment and structure
>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170} Back     alignment and structure
>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Back     alignment and structure
>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Back     alignment and structure
>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5 Back     alignment and structure
>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus} Back     alignment and structure
>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2 Back     alignment and structure
>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2 Back     alignment and structure
>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3} Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} Back     alignment and structure
>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A Back     alignment and structure
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} 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 209
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 5e-13
d1wi3a_71 a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Hom 2e-05
d1zq3p167 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fl 0.001
d1fjla_65 a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila 0.002
>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 = 60.0 bits (145), Expect = 5e-13
 Identities = 44/69 (63%), Positives = 53/69 (76%)

Query: 118 PPGNVGPATGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVL 177
              N   + G +KR RTKFT EQK+KML FAER+GWR+Q+ DDVA+ QFC E GV+R VL
Sbjct: 6   SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVL 65

Query: 178 KVWMHNNKN 186
           K+WMHNNKN
Sbjct: 66  KIWMHNNKN 74
>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]} Length = 71 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
>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 ?
Query209
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.89
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.72
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.72
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.72
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.69
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.68
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.68
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.68
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.67
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.67
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.67
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.66
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.66
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.64
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.64
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.63
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.63
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.61
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.61
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.61
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.57
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.55
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.53
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.52
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.51
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.44
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.43
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.37
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.32
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.32
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.3
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.27
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 91.72
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 90.08
d1hlva166 DNA-binding domain of centromere binding protein B 87.5
d1gyxa_76 4-oxalocrotonate tautomerase homologue YdcE {Esche 80.81
d2auwa167 Hypothetical protein NE0471 C-terminal domain {Nit 80.74
>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=99.89  E-value=2.9e-24  Score=156.83  Aligned_cols=66  Identities=65%  Similarity=1.134  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHhCcccCCCCHHHHHHHHHHhCCCCceeeeecccccccCCCC
Q 048824          126 TGKSKRQRTKFTQEQKDKMLEFAERIGWRMQRQDDVALNQFCNEVGVKRHVLKVWMHNNKNASHRR  191 (209)
Q Consensus       126 ~~~kKR~RTkFT~EQkekM~~faEk~GW~iqkpd~~~ve~fc~eiGv~r~V~KVWfhNnR~k~kk~  191 (209)
                      ..++||.||.||.+|++.|++|||+++|..+|||..++++||++|||++.||+|||||+|++.|+.
T Consensus        14 ~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~~   79 (80)
T d1wh7a_          14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             ccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCCC
Confidence            456789999999999999999999999999999999999999999999999999999999998863
>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>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
>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
>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]} 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
>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>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
>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]} 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
>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
>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]} 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
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} 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
>d1gyxa_ d.80.1.1 (A:) 4-oxalocrotonate tautomerase homologue YdcE {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Back     information, alignment and structure