Citrus Sinensis ID: 044959

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-------16
SYRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASIHRRRRHHDHEHKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCRAASVVGVKNLLAAEE
cHHHHHHHHHHHcccEEEcccccEEEcccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHccccccEEEEEEccccccccccccccccccccccccccccccc
cHHHHHHHHHHHccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHccccEEEEEEEEccccccccccccHHHHHHHHHcHHHHHHccc
SYRECRRNHAASIGryaydgcgeflkagkdgtkeafhcaacgchrsfhrkeLSLSVASIHRrrrhhdhehknykaktkrTKITEEQKSKMRRFAdklgwkpqrhdeeevgkfcgevGITRKMFKVWLnnnrrrpvpvrvpekcraASVVGVKNLLAAEE
syrecrrnhaasigryaydGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASihrrrrhhdhehknykaktkrtkiteeqkskmrrfadklgwkpqrhdeeevgkfcgevgiTRKMFKvwlnnnrrrpvpvrvpekcraasvvgvknllaaee
SYRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASIhrrrrhhdhehKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLnnnrrrpvpvrvpEKCRAASVVGVKNLLAAEE
*********AASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSV****************************************************VGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCRAASVVGVKNL*****
SYRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKE*******************************************DK**WKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRP*************************
********HAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASI**********************ITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCRAASVVGVKNLLAAEE
SYRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSF*******************************RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVP*************L*****
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
SYRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASIHRRRRHHDHEHKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPVRVPEKCRAASVVGVKNLLAAEE
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 ?
Query159 2.2.26 [Sep-21-2011]
Q9SB61220 ZF-HD homeobox protein At yes no 0.817 0.590 0.4 2e-28
Q9FKP8279 ZF-HD homeobox protein At no no 0.855 0.487 0.360 7e-26
Q9SEZ1242 Transcription factor HB29 no no 0.817 0.537 0.346 5e-22
>sp|Q9SB61|Y4466_ARATH ZF-HD homeobox protein At4g24660 OS=Arabidopsis thaliana GN=At4g24660 PE=1 SV=1 Back     alignment and function desciption
 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 66/165 (40%), Positives = 88/165 (53%), Gaps = 35/165 (21%)

Query: 2   YRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASIHR 61
           YREC +NHA +IG +A DGC EF+ +G+DGT +A  CAACGCHR+FHRKE        HR
Sbjct: 49  YRECLKNHAVNIGGHAVDGCCEFMPSGEDGTLDALKCAACGCHRNFHRKETESIGGRAHR 108

Query: 62  -----RRRHHDHEHKNY------------------------------KAKTKRTKITEEQ 86
                 R    H+   Y                                K  RTK T EQ
Sbjct: 109 VPTYYNRPPQPHQPPGYLHLTSPAAPYRPPAASGDEEDTSNPSSSGGTTKRFRTKFTAEQ 168

Query: 87  KSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131
           K KM  FA++LGW+ Q+HD+  V +FC E G+ R++ K+W++NN+
Sbjct: 169 KEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNK 213
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 ?
Query159
147776173199 hypothetical protein VITISV_044469 [Viti 0.792 0.633 0.538 1e-33
225448168243 PREDICTED: ZF-HD homeobox protein At4g24 0.817 0.534 0.429 6e-31
147776172 293 hypothetical protein VITISV_044468 [Viti 0.817 0.443 0.429 9e-31
225448170 292 PREDICTED: ZF-HD homeobox protein At4g24 0.817 0.445 0.429 1e-30
302142503 321 unnamed protein product [Vitis vinifera] 0.811 0.401 0.489 2e-30
168051086165 predicted protein [Physcomitrella patens 0.817 0.787 0.510 3e-29
302142029246 unnamed protein product [Vitis vinifera] 0.817 0.528 0.474 3e-28
224094799 296 predicted protein [Populus trichocarpa] 0.786 0.422 0.374 3e-28
356574811200 PREDICTED: ZF-HD homeobox protein At4g24 0.817 0.65 0.405 5e-28
224145148171 predicted protein [Populus trichocarpa] 0.817 0.760 0.423 1e-27
>gi|147776173|emb|CAN60986.1| hypothetical protein VITISV_044469 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 70/130 (53%), Positives = 93/130 (71%), Gaps = 4/130 (3%)

Query: 2   YRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELSLSVASIHR 61
           Y+EC  NHAASIG Y  DGCGEFLK G+DG+ +A  CAAC CHRSFHRKE  +    +  
Sbjct: 35  YKECMHNHAASIGYYTIDGCGEFLKGGEDGSPKALLCAACXCHRSFHRKENGVWSEKL-- 92

Query: 62  RRRHHDHEHKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRK 121
             R  + E +  + K  RTK+T+EQK +M  FA+++GWK  RH+++E+ KFC ++GI+R+
Sbjct: 93  --RGGETEVEMKRRKKPRTKLTKEQKERMXAFAERVGWKSHRHNDQEIRKFCSDIGISRR 150

Query: 122 MFKVWLNNNR 131
            FKVWLNNNR
Sbjct: 151 XFKVWLNNNR 160

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|225448168|ref|XP_002264250.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|147776172|emb|CAN60985.1| hypothetical protein VITISV_044468 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225448170|ref|XP_002264291.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|302142503|emb|CBI19706.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|168051086|ref|XP_001777987.1| predicted protein [Physcomitrella patens subsp. patens] gi|162670635|gb|EDQ57200.1| predicted protein [Physcomitrella patens subsp. patens] Back     alignment and taxonomy information
>gi|302142029|emb|CBI19232.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|224094799|ref|XP_002310240.1| predicted protein [Populus trichocarpa] gi|222853143|gb|EEE90690.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|356574811|ref|XP_003555538.1| PREDICTED: ZF-HD homeobox protein At4g24660-like [Glycine max] 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

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 ?
Query159
TAIR|locus:2025121309 HB33 "AT1G75240" [Arabidopsis 0.320 0.165 0.647 7.9e-33
TAIR|locus:2077957249 HB28 "homeobox protein 28" [Ar 0.320 0.204 0.627 4.3e-32
TAIR|locus:2062141262 HB24 "AT2G18350" [Arabidopsis 0.320 0.194 0.647 3.8e-31
TAIR|locus:2121989220 HB22 "AT4G24660" [Arabidopsis 0.314 0.227 0.66 7.7e-31
TAIR|locus:2168240279 HB25 "AT5G65410" [Arabidopsis 0.320 0.182 0.647 1.4e-29
TAIR|locus:2012602312 HB31 "AT1G14440" [Arabidopsis 0.358 0.182 0.561 1.9e-29
TAIR|locus:2165502242 HB27 "AT5G42780" [Arabidopsis 0.308 0.202 0.627 2.5e-28
TAIR|locus:2065304310 HB21 "homeobox protein 21" [Ar 0.314 0.161 0.56 9.7e-28
TAIR|locus:2095157 312 HB34 "AT3G28920" [Arabidopsis 0.358 0.182 0.508 1.4e-26
TAIR|locus:2026734242 ZFHD1 "AT1G69600" [Arabidopsis 0.327 0.214 0.5 1.5e-26
TAIR|locus:2025121 HB33 "AT1G75240" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 204 (76.9 bits), Expect = 7.9e-33, Sum P(2) = 7.9e-33
 Identities = 33/51 (64%), Positives = 42/51 (82%)

Query:     2 YRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKEL 52
             YREC +NHAAS+G   +DGCGEF+ +G++GT EA  CAAC CHR+FHRKE+
Sbjct:    76 YRECLKNHAASVGGSVHDGCGEFMPSGEEGTIEALRCAACDCHRNFHRKEM 126
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:2077957 HB28 "homeobox protein 28" [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:2121989 HB22 "AT4G24660" [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:2012602 HB31 "AT1G14440" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2165502 HB27 "AT5G42780" [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:2095157 HB34 "AT3G28920" [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

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
JGI60268
hypothetical protein (165 aa)
(Physcomitrella patens)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query159
pfam0477060 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation 2e-25
TIGR0156653 TIGR01566, ZF_HD_prot_N, ZF-HD homeobox protein Cy 3e-20
TIGR0156558 TIGR01565, homeo_ZF_HD, homeobox domain, ZF-HD cla 4e-16
>gnl|CDD|218256 pfam04770, ZF-HD_dimer, ZF-HD protein dimerisation region Back     alignment and domain information 
 Score = 92.0 bits (229), Expect = 2e-25
 Identities = 33/52 (63%), Positives = 43/52 (82%)

Query: 2  YRECRRNHAASIGRYAYDGCGEFLKAGKDGTKEAFHCAACGCHRSFHRKELS 53
          YREC +NHAASIG +A DGCGEF+ +G++GT ++  CAACGCHR+FHR+E  
Sbjct: 6  YRECLKNHAASIGGHAVDGCGEFMPSGEEGTPDSLKCAACGCHRNFHRREPE 57

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 159
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 99.94
KOG0843197 consensus Transcription factor EMX1 and related HO 99.67
PF0004657 Homeobox: Homeobox domain not present here.; Inter 99.65
KOG0489261 consensus Transcription factor zerknullt and relat 99.65
KOG0493342 consensus Transcription factor Engrailed, contains 99.61
KOG0488309 consensus Transcription factor BarH and related HO 99.61
KOG0484125 consensus Transcription factor PHOX2/ARIX, contain 99.56
KOG0842307 consensus Transcription factor tinman/NKX2-3, cont 99.56
smart0038956 HOX Homeodomain. DNA-binding factors that are invo 99.53
KOG2251 228 consensus Homeobox transcription factor [Transcrip 99.53
KOG0485268 consensus Transcription factor NKX-5.1/HMX1, conta 99.51
KOG0494 332 consensus Transcription factor CHX10 and related H 99.5
cd0008659 homeodomain Homeodomain; DNA binding domains invol 99.49
KOG0850245 consensus Transcription factor DLX and related pro 99.48
KOG3802398 consensus Transcription factor OCT-1, contains POU 99.44
KOG0492246 consensus Transcription factor MSH, contains HOX d 99.44
KOG0844 408 consensus Transcription factor EVX1, contains HOX 99.42
KOG0487308 consensus Transcription factor Abd-B, contains HOX 99.42
KOG4577 383 consensus Transcription factor LIM3, contains LIM 99.41
KOG0491194 consensus Transcription factor BSH, contains HOX d 99.23
KOG0483198 consensus Transcription factor HEX, contains HOX a 99.22
COG5576156 Homeodomain-containing transcription factor [Trans 99.19
KOG0490235 consensus Transcription factor, contains HOX domai 99.18
KOG0486 351 consensus Transcription factor PTX1, contains HOX 99.13
KOG0848317 consensus Transcription factor Caudal, contains HO 99.09
KOG0847288 consensus Transcription factor, contains HOX domai 99.02
KOG1168385 consensus Transcription factor ACJ6/BRN-3, contain 98.98
KOG0849354 consensus Transcription factor PRD and related pro 98.91
KOG2252558 consensus CCAAT displacement protein and related h 98.36
KOG0490235 consensus Transcription factor, contains HOX domai 98.32
KOG1146 1406 consensus Homeobox protein [General function predi 97.92
PF0592040 Homeobox_KN: Homeobox KN domain; InterPro: IPR0084 97.7
KOG0775304 consensus Transcription factor SIX and related HOX 97.45
KOG0774334 consensus Transcription factor PBX and related HOX 97.27
PF0421853 CENP-B_N: CENP-B N-terminal DNA-binding domain; In 96.71
PF0152776 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp 96.35
KOG0773342 consensus Transcription factor MEIS1 and related H 95.81
PF1156956 Homez: Homeodomain leucine-zipper encoding, Homez; 94.52
KOG3623 1007 consensus Homeobox transcription factor SIP1 [Tran 94.01
cd0056942 HTH_Hin_like Helix-turn-helix domain of Hin and re 93.58
cd0617155 Sigma70_r4 Sigma70, region (SR) 4 refers to the mo 91.56
PRK09413121 IS2 repressor TnpA; Reviewed 90.12
PF0279645 HTH_7: Helix-turn-helix domain of resolvase; Inter 89.79
PF0496753 HTH_10: HTH DNA binding domain; InterPro: IPR00705 88.92
COG2963116 Transposase and inactivated derivatives [DNA repli 87.84
PF0019658 GerE: Bacterial regulatory proteins, luxR family; 86.02
smart0042158 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo 85.96
PF06163127 DUF977: Bacterial protein of unknown function (DUF 85.92
PF0828154 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013 84.76
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 84.68
PF1393644 HTH_38: Helix-turn-helix domain; PDB: 2W48_A. 84.46
PRK06759154 RNA polymerase factor sigma-70; Validated 81.8
PRK03975141 tfx putative transcriptional regulator; Provisiona 81.61
cd0617057 LuxR_C_like C-terminal DNA-binding domain of LuxR- 81.18
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 80.7
PRK10403215 transcriptional regulator NarP; Provisional 80.39
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain Back     alignment and domain information 
Probab=100.00  E-value=1.4e-38  Score=214.85  Aligned_cols=52  Identities=63%  Similarity=1.258  Sum_probs=49.9

Q ss_pred             CcHHHhhhhhhccCCccccCcccccc-CCCCCCcccccccccccccccccccc
Q 044959            1 SYRECRRNHAASIGRYAYDGCGEFLK-AGKDGTKEAFHCAACGCHRSFHRKEL   52 (159)
Q Consensus         1 ~Y~eC~~Nhaa~~G~~~~DgC~ef~~-~~~~~~~~~l~CaaCgcHRnFHr~~~   52 (159)
                      .|+||||||||+||||+||||||||| +|+++++++|+||||||||||||||+
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            59999999999999999999999999 68899999999999999999999984

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
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription] Back     alignment and domain information
>PF00046 Homeobox: Homeobox domain not present here Back     alignment and domain information
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only] Back     alignment and domain information
>KOG0484 consensus Transcription factor PHOX2/ARIX, 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
>smart00389 HOX Homeodomain Back     alignment and domain information
>KOG2251 consensus Homeobox transcription factor [Transcription] Back     alignment and domain information
>KOG0485 consensus Transcription factor NKX-5 Back     alignment and domain information
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only] 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
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] Back     alignment and domain information
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription] Back     alignment and domain information
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription] Back     alignment and domain information
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription] Back     alignment and domain information
>KOG0491 consensus Transcription factor BSH, 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
>COG5576 Homeodomain-containing transcription factor [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription] Back     alignment and domain information
>KOG0847 consensus Transcription factor, 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
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] Back     alignment and domain information
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription] Back     alignment and domain information
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only] Back     alignment and domain information
>KOG1146 consensus Homeobox protein [General function prediction only] Back     alignment and domain information
>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
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription] Back     alignment and domain information
>KOG0774 consensus Transcription factor PBX 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
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A 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
>PRK09413 IS2 repressor TnpA; Reviewed 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
>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
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair] Back     alignment and domain information
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators Back     alignment and domain information
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon Back     alignment and domain information
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function 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
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK03975 tfx putative transcriptional regulator; Provisional Back     alignment and domain information
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK10403 transcriptional regulator NarP; Provisional 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 ?
Query159
1wh7_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 1e-10
1wh5_A80 Solution Structure Of Homeobox Domain Of Arabidopsi 5e-10
>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 = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 25/49 (51%), Positives = 36/49 (73%)
Query: 79  RTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWL 127
           RTK T EQK KM  FA++LGW+ Q+HD+  V +FC E G+ R++ K+W+
Sbjct: 21  RTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWM 69
>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 ?
Query159
1wh5_A80 ZF-HD homeobox family protein; structural genomics 6e-21
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 8e-21
>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 = 80.4 bits (198), Expect = 6e-21
 Identities = 27/58 (46%), Positives = 40/58 (68%)

Query: 74  KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNR 131
             K  RTK T EQK +M   A+++GW+ QR D+E + +FC E G+ R++ KVWL+NN+
Sbjct: 16  IRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNK 73
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query159
1wh7_A80 ZF-HD homeobox family protein; homeobox domain, st 99.92
1wh5_A80 ZF-HD homeobox family protein; structural genomics 99.91
2da4_A80 Hypothetical protein DKFZP686K21156; homeobox doma 99.82
2da3_A80 Alpha-fetoprotein enhancer binding protein; homeob 99.8
2dmq_A80 LIM/homeobox protein LHX9; homeobox domain, three 99.79
2kt0_A84 Nanog, homeobox protein nanog; homeodomain, struct 99.79
2cra_A70 Homeobox protein HOX-B13; DNA-binding, transcripti 99.79
2dmt_A80 Homeobox protein BARH-like 1; homeobox domain, thr 99.79
2djn_A70 Homeobox protein DLX-5; structural genomics, NPPSF 99.78
2da2_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.78
2vi6_A62 Homeobox protein nanog; homeodomain, DNA-binding, 99.78
2dms_A80 Homeobox protein OTX2; homeobox domain, three heli 99.77
2dmu_A70 Homeobox protein goosecoid; homeobox domain, three 99.77
2l7z_A73 Homeobox protein HOX-A13; gene regulation; NMR {Ho 99.77
2da1_A70 Alpha-fetoprotein enhancer binding protein; homeob 99.77
1wi3_A71 DNA-binding protein SATB2; homeodomain, helix-turn 99.77
2hdd_A61 Protein (engrailed homeodomain Q50K); DNA binding, 99.76
1bw5_A66 ISL-1HD, insulin gene enhancer protein ISL-1; DNA- 99.76
2h1k_A63 IPF-1, pancreatic and duodenal homeobox 1, homeodo 99.75
2e1o_A70 Homeobox protein PRH; DNA binding protein, structu 99.75
1ig7_A58 Homeotic protein MSX-1; helix-turn-helix, transcri 99.75
1ahd_P68 Antennapedia protein mutant; DNA binding protein/D 99.75
2cue_A80 Paired box protein PAX6; homeobox domain, transcri 99.75
1nk2_P77 Homeobox protein VND; homeodomain, DNA-binding pro 99.75
3rkq_A58 Homeobox protein NKX-2.5; helix-turn-helix, DNA bi 99.74
1jgg_A60 Segmentation protein EVEN-skipped; homeodomain, pr 99.74
3a01_A93 Homeodomain-containing protein; homeodomain, prote 99.74
2m0c_A75 Homeobox protein aristaless-like 4; structural gen 99.74
1b8i_A81 Ultrabithorax, protein (ultrabithorax homeotic pro 99.73
1akh_A61 Protein (mating-type protein A-1); complex (TWO DN 99.73
2dn0_A76 Zinc fingers and homeoboxes protein 3; triple home 99.73
1ftt_A68 TTF-1 HD, thyroid transcription factor 1 homeodoma 99.73
1zq3_P68 PRD-4, homeotic bicoid protein; protein-DNA comple 99.73
1yz8_P68 Pituitary homeobox 2; DNA binding protein, transcr 99.73
1puf_A77 HOX-1.7, homeobox protein HOX-A9; homeodomian, pro 99.73
1du6_A64 PBX1, homeobox protein PBX1; homeodomain, gene reg 99.72
2hi3_A73 Homeodomain-only protein; transcription; NMR {Mus 99.72
2r5y_A88 Homeotic protein sex combs reduced; homeodomain; H 99.72
2k40_A67 Homeobox expressed in ES cells 1; thermostable hom 99.72
2ly9_A74 Zinc fingers and homeoboxes protein 1; structural 99.72
1fjl_A81 Paired protein; DNA-binding protein, paired BOX, t 99.71
1uhs_A72 HOP, homeodomain only protein; structural genomics 99.71
2ecc_A76 Homeobox and leucine zipper protein homez; homeobo 99.7
3nar_A96 ZHX1, zinc fingers and homeoboxes protein 1; corep 99.7
3a02_A60 Homeobox protein aristaless; homeodomain, developm 99.7
2da5_A75 Zinc fingers and homeoboxes protein 3; homeobox do 99.7
1b72_A97 Protein (homeobox protein HOX-B1); homeodomain, DN 99.69
1x2n_A73 Homeobox protein pknox1; homeobox domain, structur 99.69
2cuf_A95 FLJ21616 protein; homeobox domain, hepatocyte tran 99.68
1puf_B73 PRE-B-cell leukemia transcription factor-1; homeod 99.68
1au7_A146 Protein PIT-1, GHF-1; complex (DNA-binding protein 99.67
3d1n_I151 POU domain, class 6, transcription factor 1; prote 99.67
1e3o_C160 Octamer-binding transcription factor 1; transcript 99.67
2dmn_A83 Homeobox protein TGIF2LX; TGFB-induced factor 2-li 99.66
3a03_A56 T-cell leukemia homeobox protein 2; homeodomain, d 99.66
1mnm_C87 Protein (MAT alpha-2 transcriptional repressor); t 99.66
2xsd_C164 POU domain, class 3, transcription factor 1; trans 99.65
1b72_B87 Protein (PBX1); homeodomain, DNA, complex, DNA-bin 99.65
1k61_A60 Mating-type protein alpha-2; protein-DNA complex, 99.65
1lfb_A99 Liver transcription factor (LFB1); transcription r 99.65
2d5v_A164 Hepatocyte nuclear factor 6; transcription factor, 99.64
2ecb_A89 Zinc fingers and homeoboxes protein 1; homeobox do 99.64
1le8_B83 Mating-type protein alpha-2; matalpha2, isothermal 99.63
2dmp_A89 Zinc fingers and homeoboxes protein 2; homeobox do 99.63
2da6_A102 Hepatocyte nuclear factor 1-beta; homeobox domain, 99.62
2cqx_A72 LAG1 longevity assurance homolog 5; homeodomain, D 99.61
2e19_A64 Transcription factor 8; homeobox domain, structura 99.6
3l1p_A155 POU domain, class 5, transcription factor 1; POU, 99.59
3nau_A66 Zinc fingers and homeoboxes protein 2; ZHX2, corep 99.55
2l9r_A69 Homeobox protein NKX-3.1; structural genomics, nor 99.54
1x2m_A64 LAG1 longevity assurance homolog 6; homeobox domai 99.47
1ic8_A194 Hepatocyte nuclear factor 1-alpha; transcription r 99.44
3k2a_A67 Homeobox protein MEIS2; homeobox domain, DNA-bindi 99.43
2h8r_A221 Hepatocyte nuclear factor 1-beta; trasncription fa 99.36
2da7_A71 Zinc finger homeobox protein 1B; homeobox domain, 99.32
1mh3_A421 Maltose binding-A1 homeodomain protein chimera; MA 99.32
2lk2_A89 Homeobox protein TGIF1; NESG, structural genomics, 99.07
2nzz_A37 Penetratin conjugated GAS (374-394) peptide; confo 98.13
2elh_A87 CG11849-PA, LD40883P; structural genomics, NPPSFA, 95.6
2glo_A59 Brinker CG9653-PA; protein-DNA complex, helix-turn 95.32
1hlv_A131 CENP-B, major centromere autoantigen B; helix-turn 94.93
2jn6_A97 Protein CGL2762, transposase; GFT PSI-2, protein s 93.81
1tc3_C51 Protein (TC3 transposase); DNA binding, helix-turn 93.44
2ys9_A70 Homeobox and leucine zipper protein homez; homeodo 93.25
1jko_C52 HIN recombinase, DNA-invertase HIN; water-mediated 92.98
2rn7_A108 IS629 ORFA; helix, all alpha, unknown function, st 92.64
1iuf_A144 Centromere ABP1 protein; riken structural genomics 90.52
1je8_A82 Nitrate/nitrite response regulator protein NARL; p 90.41
2ofy_A86 Putative XRE-family transcriptional regulator; tra 90.25
3c57_A95 Two component transcriptional regulatory protein; 89.24
1pdn_C128 Protein (PRD paired); protein-DNA complex, double 88.17
1u78_A141 TC3 transposase, transposable element TC3 transpos 87.46
1k78_A149 Paired box protein PAX5; paired domain, ETS domain 86.58
1x3u_A79 Transcriptional regulatory protein FIXJ; helix-tur 85.71
1p4w_A99 RCSB; solution structure, DNA binding domain, DNA 85.65
3kz3_A80 Repressor protein CI; five helix bundle, DNA-bindi 85.28
2k27_A159 Paired box protein PAX-8; paired domain, solution 85.27
2rnj_A91 Response regulator protein VRAR; HTH LUXR-type dom 84.57
1fse_A74 GERE; helix-turn-helix DNA-binding protein transcr 84.51
2ao9_A155 Phage protein; structural genomics, nine-fold NCS. 83.89
3ulq_B90 Transcriptional regulatory protein COMA; tetratric 83.18
2p7v_B68 Sigma-70, RNA polymerase sigma factor RPOD; RSD, r 82.88
3hug_A92 RNA polymerase sigma factor; ECF sigma factor, zin 82.25
3clo_A258 Transcriptional regulator; NP_811094.1, bacterial 81.18
3bdn_A 236 Lambda repressor; repressor, allostery; HET: DNA; 80.76
>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=99.92  E-value=4.6e-25  Score=156.16  Aligned_cols=67  Identities=42%  Similarity=0.793  Sum_probs=63.3

Q ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCC
Q 044959           70 HKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVP  136 (159)
Q Consensus        70 ~~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk  136 (159)
                      ....++||.||.||.+|++.|+.|++++||+.+|||..++++||.+|||++.||||||||+|+|+++
T Consensus        12 ~~~~~~rR~Rt~ft~~Ql~~Le~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            3455689999999999999999999999999999999999999999999999999999999999987
>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
>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
>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
>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
>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
>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
>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
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A* Back     alignment and structure
>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
>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
>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
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus} 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
>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
>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
>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
>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
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens} Back     alignment and structure
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 Back     alignment and structure
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster} 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
>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
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A* Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>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
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens} Back     alignment and structure
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A Back     alignment and structure
>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
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens} Back     alignment and structure
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1 Back     alignment and structure
>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
>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
>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
>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
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B* Back     alignment and structure
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 Back     alignment and structure
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Back     alignment and structure
>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
>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
>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
>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
>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
>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
>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A Back     alignment and structure
>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti} 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
>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda} 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
>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
>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
>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
>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A 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
>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis} Back     alignment and structure
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482} Back     alignment and structure
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {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 159
d1wh7a_80 a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Tha 1e-08
>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 = 46.9 bits (111), Expect = 1e-08
 Identities = 28/60 (46%), Positives = 41/60 (68%)

Query: 74  KAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRR 133
             K  RTK T EQK KM  FA++LGW+ Q+HD+  V +FC E G+ R++ K+W++NN+  
Sbjct: 16  TTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNS 75

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query159
d1wh7a_80 ZF-HD homeobox protein At4g24660 {Thale cress (Ara 99.92
d2craa158 Homeobox protein hox-b13 {Human (Homo sapiens) [Ta 99.82
d1vnda_77 VND/NK-2 protein {Fruit fly (Drosophila melanogast 99.82
d1p7ia_53 Engrailed Homeodomain {Drosophila melanogaster [Ta 99.8
d1ig7a_58 Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10 99.8
d1jgga_57 Even-skipped homeodomain {Fruit fly (Drosophila me 99.79
d2e1oa157 Homeobox protein prh {Human (Homo sapiens) [TaxId: 99.79
d1ocpa_67 Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId 99.77
d1ftta_68 Thyroid transcription factor 1 homeodomain {Rat (R 99.77
d1wi3a_71 DNA-binding protein SATB2 {Human (Homo sapiens) [T 99.77
d1pufa_77 Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax 99.77
d9anta_56 Antennapedia Homeodomain {Drosophila melanogaster 99.77
d1zq3p167 Homeotic bicoid protein {Fruit fly (Drosophila mel 99.77
d1fjla_65 Paired protein {Fruit fly (Drosophila melanogaster 99.77
d1bw5a_66 Insulin gene enhancer protein isl-1 {Rat (Rattus n 99.76
d2cuea168 Paired box protein pax6 {Human (Homo sapiens) [Tax 99.76
d1uhsa_72 Homeodomain-only protein, Hop {Mouse (Mus musculus 99.75
d1b72a_88 Homeobox protein hox-b1 {Human (Homo sapiens) [Tax 99.75
d1au7a158 Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta 99.74
d1yz8p160 Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 99.73
d1le8a_53 Mating type protein A1 Homeodomain {Baker's yeast 99.72
d1s7ea150 Hepatocyte nuclear factor 6 {Mouse (Mus musculus) 99.7
d1e3oc157 Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId 99.69
d2cufa182 Homeobox-containing protein 1, HMBOX1 (Flj21616) { 99.69
d1pufb_73 pbx1 {Human (Homo sapiens) [TaxId: 9606]} 99.64
d2ecca176 Homeobox-leucine zipper protein Homez {Human (Homo 99.62
d2ecba176 Zinc fingers and homeoboxes protein 1, ZHX1 {Human 99.6
d1x2na162 Homeobox protein pknox1 {Human (Homo sapiens) [Tax 99.53
d1lfba_78 Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat 99.53
d1x2ma152 Lag1 longevity assurance homolog 6, LASS6 {Mouse ( 99.51
d1k61a_60 mat alpha2 Homeodomain {Baker's yeast (Saccharomyc 99.51
d2cqxa159 LAG1 longevity assurance homolog 5, LASS5 {Mouse ( 99.48
d1ijwc_47 HIN recombinase (DNA-binding domain) {Synthetic} 94.21
d1hlva166 DNA-binding domain of centromere binding protein B 93.41
d2jn6a189 Uncharacterized protein Cgl2762 {Corynebacterium g 92.69
d1bl0a154 MarA {Escherichia coli [TaxId: 562]} 84.5
>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=99.92  E-value=2e-25  Score=156.71  Aligned_cols=69  Identities=41%  Similarity=0.767  Sum_probs=64.1

Q ss_pred             CCCCCCCCCCCccCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCccchhhhhccccCCCCCC
Q 044959           69 EHKNYKAKTKRTKITEEQKSKMRRFADKLGWKPQRHDEEEVGKFCGEVGITRKMFKVWLNNNRRRPVPV  137 (159)
Q Consensus        69 ~~~~~~kKR~RTkFT~eQkekLe~ffek~GW~iq~~d~~~r~efc~eiGl~r~VvKVWFqNrR~k~kk~  137 (159)
                      .....++||.||.||.+|++.|++|||+++|..+|||..++++||.+|||++.||+|||||+|++.|+.
T Consensus        11 ~~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~~   79 (80)
T d1wh7a_          11 SSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPSS   79 (80)
T ss_dssp             CCCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCCC
T ss_pred             CCCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCCC
Confidence            344556789999999999999999999999999999999999999999999999999999999999863
>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {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
>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]} Back     information, alignment and structure
>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>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
>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]} 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
>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
>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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
>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>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
>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} 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
>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {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
>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>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
>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]} Back     information, alignment and structure
>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure