Citrus Sinensis ID: 024081

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270--
MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLSTPQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPADTVQEAAAAAAGQVADAENKSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
cccccccccHHHHHHHHHHHHHHccccHHHHHccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEc
cccccccccHHHHHHHHHHHHHcccccHHHHHccccHHHHHHccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEccEEEccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEc
mgnpkqkwTAEEEEALRAGVAkhgtgkwkniqrdpefnpflfsrsnidlkdkwrnmsvsapreksrtlkpkagsdapavplstpqtsalpaavpidasadpitdesarssapkYNALIFEAISAlkepngsdVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFkvkedaslgtktpnpkqkdtrpkllhstndvspadTVQEAAAAAAGQVADAENKSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERcsrgeivvva
mgnpkqkwtAEEEEALRAGVakhgtgkwkniqrdpefnpflfsrsnidlkdkwrnmsvsapreksrtlkpkagsdapaVPLSTPQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEqrlevppnFRRLLSSRLRRLVAQEKLEKVqncfkvkedaslgtktpnpkqkdtrpklLHSTNDVSPADTVQEAAAAAAGQVADAENKSFVAAEAVKEAervsrmaedtdSLLQLAKEIfercsrgeivvva
MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLSTPQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFrrllssrlrrlVAQEKLEKVQNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPadtvqeaaaaaagqvadaeNKSFvaaeavkeaervSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
**************************KWKNIQ***EFNPFLFSRSNI******************************************************************YNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFK*****************************************************************************LQLAKEIFERCSRGEIV***
**NPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKP********************************TDESARSSAPKYNALIFEAISALK***GSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLE***********************************************************************ERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
*************EALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMS***************************QTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKEDASL**************KLLHSTNDVSPADTVQ**************NKSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
******KWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV****************************************************APKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKE******************************DTVQE******GQVADAENKSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
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MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSAPREKSRTLKPKAGSDAPAVPLSTPQTSALPAAVPIDASADPITDESARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPxxxxxxxxxxxxxxxxxxxxxSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA
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 ?
Query272 2.2.26 [Sep-21-2011]
F4IEY4287 Telomere repeat-binding f yes no 0.985 0.933 0.491 6e-60
F4I7L1296 Telomere repeat-binding f no no 0.992 0.912 0.476 7e-53
Q8VWK4300 Telomere repeat-binding f no no 0.632 0.573 0.443 1e-34
Q9M2X3295 Telomere repeat-binding f no no 0.654 0.603 0.407 9e-30
Q9FJW5299 Telomere repeat-binding f no no 0.647 0.588 0.406 2e-29
P26569273 Histone H1.2 OS=Arabidops no no 0.338 0.336 0.431 1e-10
P23444246 Histone H1 OS=Zea mays PE N/A no 0.231 0.256 0.446 4e-09
P27806238 Histone H1 OS=Triticum ae N/A no 0.238 0.273 0.417 4e-08
Q9PU53718 Telomeric repeat-binding yes no 0.191 0.072 0.428 2e-06
Q15554500 Telomeric repeat-binding yes no 0.176 0.096 0.461 3e-06
>sp|F4IEY4|TRB5_ARATH Telomere repeat-binding factor 5 OS=Arabidopsis thaliana GN=At1g72740 PE=2 SV=1 Back     alignment and function desciption
 Score =  231 bits (588), Expect = 6e-60,   Method: Compositional matrix adjust.
 Identities = 143/291 (49%), Positives = 186/291 (63%), Gaps = 23/291 (7%)

Query: 1   MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSV-- 58
           MGN K KWTAEEEEAL AG+ KHG GKWKNI RDPEF   L  RSNIDLKDKWRN+SV  
Sbjct: 1   MGNQKLKWTAEEEEALLAGIRKHGPGKWKNILRDPEFADQLIHRSNIDLKDKWRNLSVPP 60

Query: 59  --SAPREKSRTLKPKAGSDAP------AVPLSTPQTSALPAAVPIDASADPITDESARSS 110
              +   K+R  K K   D P      AV +  P  +  P        ++ I DE+ + +
Sbjct: 61  GTQSLTNKARPAKVKEEGDTPAADANDAVTIPRPIPTIPPPPGRRTLPSELIPDENTK-N 119

Query: 111 APKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKV 170
           AP+Y+ +IFEA+SAL + NGSDVS+I  +IE R EVPPNFRR+LS+RLRRL AQ KLEKV
Sbjct: 120 APRYDGVIFEALSALADGNGSDVSSIYHFIEPRHEVPPNFRRILSTRLRRLAAQSKLEKV 179

Query: 171 ------QNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPADT---VQEAAAAAAGQ 221
                 QN +K+ + +  GTK   PK K+T  KL  + N  S AD+   ++EAA  AA +
Sbjct: 180 STFKSIQNFYKIPDPS--GTKIGVPKPKETHTKLRQANNQTS-ADSQQMIEEAAITAACK 236

Query: 222 VADAENKSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA 272
           V +AENK  VA  A +E E+++++AE+   LL +A E+ E CS GE +++A
Sbjct: 237 VVEAENKIDVAKLAAEEFEKMTKIAEENRKLLVIATEMHELCSCGETMLLA 287
Binds preferentially double-stranded telomeric repeats.
Arabidopsis thaliana (taxid: 3702)
>sp|F4I7L1|TRB4_ARATH Telomere repeat-binding factor 4 OS=Arabidopsis thaliana GN=At1g17520 PE=2 SV=2 Back     alignment and function description
>sp|Q8VWK4|TRB1_ARATH Telomere repeat-binding factor 1 OS=Arabidopsis thaliana GN=TRB1 PE=1 SV=1 Back     alignment and function description
>sp|Q9M2X3|TRB3_ARATH Telomere repeat-binding factor 3 OS=Arabidopsis thaliana GN=TRB3 PE=1 SV=1 Back     alignment and function description
>sp|Q9FJW5|TRB2_ARATH Telomere repeat-binding factor 2 OS=Arabidopsis thaliana GN=TRB2 PE=1 SV=1 Back     alignment and function description
>sp|P26569|H12_ARATH Histone H1.2 OS=Arabidopsis thaliana GN=At2g30620 PE=1 SV=1 Back     alignment and function description
>sp|P23444|H1_MAIZE Histone H1 OS=Zea mays PE=2 SV=2 Back     alignment and function description
>sp|P27806|H1_WHEAT Histone H1 OS=Triticum aestivum PE=2 SV=2 Back     alignment and function description
>sp|Q9PU53|TERF2_CHICK Telomeric repeat-binding factor 2 OS=Gallus gallus GN=TERF2 PE=1 SV=2 Back     alignment and function description
>sp|Q15554|TERF2_HUMAN Telomeric repeat-binding factor 2 OS=Homo sapiens GN=TERF2 PE=1 SV=2 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 ?
Query272
255546151283 DNA binding protein, putative [Ricinus c 0.992 0.954 0.715 2e-99
224122558279 single myb histone [Populus trichocarpa] 0.988 0.964 0.684 1e-93
224087971275 single myb histone [Populus trichocarpa] 0.977 0.967 0.683 2e-90
225444861281 PREDICTED: uncharacterized protein LOC10 0.992 0.960 0.685 2e-87
449458153279 PREDICTED: telomere repeat-binding facto 0.977 0.953 0.592 2e-78
307135862279 MYB transcription factor [Cucumis melo s 0.977 0.953 0.589 9e-78
356522138285 PREDICTED: uncharacterized protein LOC78 0.966 0.922 0.564 2e-76
255560719349 transcription factor, putative [Ricinus 0.977 0.762 0.606 2e-75
351722098281 MYB transcription factor MYB107 [Glycine 0.963 0.932 0.556 8e-75
302398965303 MYBR domain class transcription factor [ 0.911 0.818 0.504 2e-74
>gi|255546151|ref|XP_002514135.1| DNA binding protein, putative [Ricinus communis] gi|223546591|gb|EEF48089.1| DNA binding protein, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  368 bits (944), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 204/285 (71%), Positives = 238/285 (83%), Gaps = 15/285 (5%)

Query: 1   MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
           MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQ+DPEFNPFLFSRSNIDLKDKWRNMSVSA
Sbjct: 1   MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQKDPEFNPFLFSRSNIDLKDKWRNMSVSA 60

Query: 61  PREKSRTLKPKAGSDAPA-------VPLSTPQTSA-LPAAVPIDASADPITDESARS--- 109
             EKSRT KPKA SD P        +P+S  Q+SA +    P+D  ADP+ D+S ++   
Sbjct: 61  -GEKSRTPKPKANSDIPPATKAVSPIPVSNLQSSASVITTSPLD-EADPMVDDSTKTFGD 118

Query: 110 --SAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKL 167
             +APKYNA+IFEAISAL + +G+D +AI+SYIEQR  VP NFRR LSSRLRRLVAQEKL
Sbjct: 119 AKTAPKYNAMIFEAISALNKQHGADTTAIVSYIEQRQVVPQNFRRQLSSRLRRLVAQEKL 178

Query: 168 EKVQNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPADTVQEAAAAAAGQVADAEN 227
           EKVQNCFK+K ++SL TKTP PKQKD RP+ L ST+ ++  DT++EAA AAA ++A+AEN
Sbjct: 179 EKVQNCFKIKNNSSLETKTPTPKQKDVRPRHLQSTSCINSGDTMEEAAVAAAYRIAEAEN 238

Query: 228 KSFVAAEAVKEAERVSRMAEDTDSLLQLAKEIFERCSRGEIVVVA 272
           KSFVAAEAVKEAERVS+MAEDTDSLLQLAKEIFE+CSRGE+V++A
Sbjct: 239 KSFVAAEAVKEAERVSKMAEDTDSLLQLAKEIFEKCSRGEVVLIA 283

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224122558|ref|XP_002330511.1| single myb histone [Populus trichocarpa] gi|222872445|gb|EEF09576.1| single myb histone [Populus trichocarpa] Back     alignment and taxonomy information
>gi|224087971|ref|XP_002308277.1| single myb histone [Populus trichocarpa] gi|222854253|gb|EEE91800.1| single myb histone [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225444861|ref|XP_002281183.1| PREDICTED: uncharacterized protein LOC100254369 [Vitis vinifera] gi|297738637|emb|CBI27882.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449458153|ref|XP_004146812.1| PREDICTED: telomere repeat-binding factor 5-like [Cucumis sativus] gi|449476637|ref|XP_004154792.1| PREDICTED: telomere repeat-binding factor 5-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|307135862|gb|ADN33730.1| MYB transcription factor [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|356522138|ref|XP_003529706.1| PREDICTED: uncharacterized protein LOC780537 [Glycine max] Back     alignment and taxonomy information
>gi|255560719|ref|XP_002521373.1| transcription factor, putative [Ricinus communis] gi|223539451|gb|EEF41041.1| transcription factor, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|351722098|ref|NP_001237744.1| MYB transcription factor MYB107 [Glycine max] gi|110931702|gb|ABH02850.1| MYB transcription factor MYB107 [Glycine max] Back     alignment and taxonomy information
>gi|302398965|gb|ADL36777.1| MYBR domain class transcription factor [Malus x domestica] 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 ?
Query272
TAIR|locus:2030275287 AT1G72740 [Arabidopsis thalian 0.988 0.937 0.410 9.1e-45
TAIR|locus:2007878296 AT1G17520 [Arabidopsis thalian 0.632 0.581 0.521 3.4e-38
TAIR|locus:2031095300 TRB1 "telomere repeat binding 0.676 0.613 0.397 2.1e-29
TAIR|locus:2158611299 TRB2 "AT5G67580" [Arabidopsis 0.544 0.494 0.465 2.2e-27
TAIR|locus:2097325295 TRB3 "telomere repeat binding 0.540 0.498 0.45 5.2e-26
TAIR|locus:2020193197 AT1G54260 [Arabidopsis thalian 0.330 0.456 0.362 5.2e-16
TAIR|locus:2064332273 AT2G30620 [Arabidopsis thalian 0.419 0.417 0.368 3.4e-07
UNIPROTKB|Q6T804426 AID1 "ANTHER INDEHISCENCE1" [O 0.176 0.112 0.538 1.3e-06
ZFIN|ZDB-GENE-090612-2386 terf1 "telomeric repeat bindin 0.169 0.119 0.46 5.5e-06
TAIR|locus:2161233448 AT5G58340 [Arabidopsis thalian 0.180 0.109 0.5 7.1e-06
TAIR|locus:2030275 AT1G72740 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 119/290 (41%), Positives = 152/290 (52%)

Query:     1 MGNPKQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
             MGN K KWTAEEEEAL AG+ KHG GKWKNI RDPEF   L  RSNIDLKDKWRN+SV  
Sbjct:     1 MGNQKLKWTAEEEEALLAGIRKHGPGKWKNILRDPEFADQLIHRSNIDLKDKWRNLSVPP 60

Query:    61 PRE----KSRTLKPKAGSDAPAVPLSTPQTSALPA-AVPIDAS-----ADPITDESARSS 110
               +    K+R  K K   D PA   +   T   P   +P         ++ I DE+ ++ 
Sbjct:    61 GTQSLTNKARPAKVKEEGDTPAADANDAVTIPRPIPTIPPPPGRRTLPSELIPDENTKN- 119

Query:   111 APKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFXXXXXXXXXXXVAQEKLEKV 170
             AP+Y+ +IFEA+SAL + NGSDVS+I  +IE R EVPPNF            AQ KLEKV
Sbjct:   120 APRYDGVIFEALSALADGNGSDVSSIYHFIEPRHEVPPNFRRILSTRLRRLAAQSKLEKV 179

Query:   171 ------QNCFKVKEDASLGTKTPNPKQKDTRPKLLHSTNDVSPXXXXXXXXXXXXXX--X 222
                   QN +K+ + +  GTK   PK K+T  KL  + N  S                  
Sbjct:   180 STFKSIQNFYKIPDPS--GTKIGVPKPKETHTKLRQANNQTSADSQQMIEEAAITAACKV 237

Query:   223 XXXXNKSFXXXXXXXXXXXXSRMAEDTDSLLQLAKEIFERCSRGEIVVVA 272
                 NK              +++AE+   LL +A E+ E CS GE +++A
Sbjct:   238 VEAENKIDVAKLAAEEFEKMTKIAEENRKLLVIATEMHELCSCGETMLLA 287
GO:0000786 "nucleosome" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM;IEA;IDA
GO:0006334 "nucleosome assembly" evidence=IEA
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
TAIR|locus:2007878 AT1G17520 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2031095 TRB1 "telomere repeat binding factor 1" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2158611 TRB2 "AT5G67580" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2097325 TRB3 "telomere repeat binding factor 3" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2020193 AT1G54260 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2064332 AT2G30620 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|Q6T804 AID1 "ANTHER INDEHISCENCE1" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-090612-2 terf1 "telomeric repeat binding factor (NIMA-interacting) 1" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
TAIR|locus:2161233 AT5G58340 [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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
F4IEY4TRB5_ARATHNo assigned EC number0.49140.98520.9337yesno

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 ?
Query272
cd1166050 cd11660, SANT_TRF, Telomere repeat binding factor- 7e-21
smart0052666 smart00526, H15, Domain in histone families 1 and 2e-19
smart0071749 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII 1e-10
cd0016745 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA- 4e-10
pfam0024947 pfam00249, Myb_DNA-binding, Myb-like DNA-binding d 4e-09
cd0007388 cd00073, H15, linker histone 1 and histone 5 domai 5e-09
pfam0053877 pfam00538, Linker_histone, linker histone H1 and H 2e-08
pfam1392159 pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding do 4e-05
>gnl|CDD|212558 cd11660, SANT_TRF, Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family Back     alignment and domain information 
 Score = 83.0 bits (206), Expect = 7e-21
 Identities = 26/51 (50%), Positives = 36/51 (70%), Gaps = 3/51 (5%)

Query: 6  QKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
          +KWT EE+EAL  GV K+G G W  I +D     F+ +R+++DLKDKWRN+
Sbjct: 1  RKWTDEEDEALVEGVEKYGVGNWAKILKDY---FFVNNRTSVDLKDKWRNL 48

Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1. Length = 50
>gnl|CDD|197772 smart00526, H15, Domain in histone families 1 and 5 Back     alignment and domain information
>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains Back     alignment and domain information
>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains Back     alignment and domain information
>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain Back     alignment and domain information
>gnl|CDD|238028 cd00073, H15, linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber Back     alignment and domain information
>gnl|CDD|215982 pfam00538, Linker_histone, linker histone H1 and H5 family Back     alignment and domain information
>gnl|CDD|206092 pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 272
cd0007388 H15 linker histone 1 and histone 5 domains; the ba 99.84
smart0052666 H15 Domain in histone families 1 and 5. 99.84
PF0053877 Linker_histone: linker histone H1 and H5 family; I 99.84
KOG4012243 consensus Histone H1 [Chromatin structure and dyna 99.51
PF0024948 Myb_DNA-binding: Myb-like DNA-binding domain; Inte 99.25
PLN03212249 Transcription repressor MYB5; Provisional 99.02
smart0071749 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi 98.98
cd0016745 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do 98.86
PF1392160 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 98.81
PLN03091 459 hypothetical protein; Provisional 98.8
PLN03212249 Transcription repressor MYB5; Provisional 98.66
KOG0048238 consensus Transcription factor, Myb superfamily [T 98.64
PLN03091 459 hypothetical protein; Provisional 98.4
KOG0048238 consensus Transcription factor, Myb superfamily [T 97.87
TIGR0155757 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c 97.81
KOG0051607 consensus RNA polymerase I termination factor, Myb 97.47
KOG0049 939 consensus Transcription factor, Myb superfamily [T 97.35
KOG0457 438 consensus Histone acetyltransferase complex SAGA/A 97.1
PF1383790 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; 96.94
KOG0049 939 consensus Transcription factor, Myb superfamily [T 96.88
PF09111118 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain 96.41
PF1387378 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain 95.91
KOG1279506 consensus Chromatin remodeling factor subunit and 95.21
PF13325199 MCRS_N: N-terminal region of micro-spherule protei 95.05
KOG0050 617 consensus mRNA splicing protein CDC5 (Myb superfam 95.0
PLN031421033 Probable chromatin-remodeling complex ATPase chain 94.82
COG5147512 REB1 Myb superfamily proteins, including transcrip 94.57
PF08074173 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR01295 94.24
COG5259531 RSC8 RSC chromatin remodeling complex subunit RSC8 93.53
PF0025096 Fork_head: Fork head domain; InterPro: IPR001766 T 92.78
PF1026480 Stork_head: Winged helix Storkhead-box1 domain; In 92.6
COG5114 432 Histone acetyltransferase complex SAGA/ADA, subuni 92.59
cd0005978 FH Forkhead (FH), also known as a "winged helix". 92.47
PF1433892 Mrr_N: Mrr N-terminal domain 92.14
COG5147 512 REB1 Myb superfamily proteins, including transcrip 91.27
KOG4282345 consensus Transcription factor GT-2 and related pr 90.57
smart0033989 FH FORKHEAD. FORKHEAD, also known as a "winged hel 89.82
KOG03841373 consensus Chromodomain-helicase DNA-binding protei 89.24
PF0891465 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR0150 87.87
KOG0051607 consensus RNA polymerase I termination factor, Myb 86.46
KOG2656445 consensus DNA methyltransferase 1-associated prote 85.28
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber Back     alignment and domain information 
Probab=99.84  E-value=4.3e-21  Score=149.92  Aligned_cols=71  Identities=42%  Similarity=0.649  Sum_probs=67.0

Q ss_pred             CCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCC-ccHHHHHHHHHHhhhccCceeeec-----cccccCCc
Q 024081          109 SSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVP-PNFRRLLSSRLRRLVAQEKLEKVQ-----NCFKVKED  179 (272)
Q Consensus       109 ~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~-~nf~~~L~~~LKrlV~~GkLvkvK-----~sykl~~~  179 (272)
                      .+||+|.+||+|||.+|+||+|||+++|++||+++|.+. ++|+.+|+.+|+++|++|.|++++     |+|+|++.
T Consensus         2 ~~hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~~~   78 (88)
T cd00073           2 PSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSKK   78 (88)
T ss_pred             CCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeCCC
Confidence            579999999999999999999999999999999999764 999999999999999999999999     89999743

>smart00526 H15 Domain in histone families 1 and 5 Back     alignment and domain information
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication) Back     alignment and domain information
>KOG4012 consensus Histone H1 [Chromatin structure and dynamics] Back     alignment and domain information
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins Back     alignment and domain information
>PLN03212 Transcription repressor MYB5; Provisional Back     alignment and domain information
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains Back     alignment and domain information
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains Back     alignment and domain information
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A Back     alignment and domain information
>PLN03091 hypothetical protein; Provisional Back     alignment and domain information
>PLN03212 Transcription repressor MYB5; Provisional Back     alignment and domain information
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>PLN03091 hypothetical protein; Provisional Back     alignment and domain information
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class Back     alignment and domain information
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription] Back     alignment and domain information
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics] Back     alignment and domain information
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A Back     alignment and domain information
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription] Back     alignment and domain information
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices Back     alignment and domain information
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain Back     alignment and domain information
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics] Back     alignment and domain information
>PF13325 MCRS_N: N-terminal region of micro-spherule protein Back     alignment and domain information
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional Back     alignment and domain information
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning] Back     alignment and domain information
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [] Back     alignment and domain information
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription] Back     alignment and domain information
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors [] Back     alignment and domain information
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia [] Back     alignment and domain information
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics] Back     alignment and domain information
>cd00059 FH Forkhead (FH), also known as a "winged helix" Back     alignment and domain information
>PF14338 Mrr_N: Mrr N-terminal domain Back     alignment and domain information
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning] Back     alignment and domain information
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription] Back     alignment and domain information
>smart00339 FH FORKHEAD Back     alignment and domain information
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription] Back     alignment and domain information
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif Back     alignment and domain information
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription] Back     alignment and domain information
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription] 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 ?
Query272
3sjm_A64 Crystal Structure Analysis Of Trf2-Dbd-Dna Complex 8e-07
1xg1_A67 Solution Structure Of Myb-Domain Of Human Trf2 Leng 1e-06
1w0u_A55 Htrf2 Dna-Binding Domain In Complex With Telomeric 2e-06
1vf9_A64 Solution Structure Of Human Trf2 Length = 64 2e-06
1vfc_A63 Solution Structure Of The Dna Complex Of Human Trf2 3e-06
1ba5_A53 Dna-Binding Domain Of Human Telomeric Protein, Htrf 5e-06
1w0t_A53 Htrf1 Dna-Binding Domain In Complex With Telomeric 6e-06
1ity_A69 Solution Structure Of The Dna Binding Domain Of Hum 1e-05
1iv6_A70 Solution Structure Of The Dna Complex Of Human Trf1 3e-05
>pdb|3SJM|A Chain A, Crystal Structure Analysis Of Trf2-Dbd-Dna Complex Length = 64 Back     alignment and structure 
Iteration: 1

 Score = 50.8 bits (120), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 24/52 (46%), Positives = 35/52 (67%), Gaps = 4/52 (7%)
Query: 5  KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNM 56
          KQKWT EE E ++AGV K+G G W  I ++    PF+ +R+ + +KD+WR M
Sbjct: 11 KQKWTVEESEWVKAGVQKYGEGNWAAISKN---YPFV-NRTAVMIKDRWRTM 58
>pdb|1XG1|A Chain A, Solution Structure Of Myb-Domain Of Human Trf2 Length = 67 Back     alignment and structure
>pdb|1W0U|A Chain A, Htrf2 Dna-Binding Domain In Complex With Telomeric Dna. Length = 55 Back     alignment and structure
>pdb|1VF9|A Chain A, Solution Structure Of Human Trf2 Length = 64 Back     alignment and structure
>pdb|1VFC|A Chain A, Solution Structure Of The Dna Complex Of Human Trf2 Length = 63 Back     alignment and structure
>pdb|1BA5|A Chain A, Dna-Binding Domain Of Human Telomeric Protein, Htrf1, Nmr, 18 Structures Length = 53 Back     alignment and structure
>pdb|1W0T|A Chain A, Htrf1 Dna-Binding Domain In Complex With Telomeric Dna. Length = 53 Back     alignment and structure
>pdb|1ITY|A Chain A, Solution Structure Of The Dna Binding Domain Of Human Trf1 Length = 69 Back     alignment and structure
>pdb|1IV6|A Chain A, Solution Structure Of The Dna Complex Of Human Trf1 Length = 70 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 ?
Query272
1w0u_A55 Telomeric repeat binding factor 2; telomere, DNA-b 1e-21
1w0t_A53 Telomeric repeat binding factor 1; telomere, DNA-b 4e-21
1vf9_A64 Telomeric repeat binding factor 2; MYB, helix-turn 6e-21
1ity_A69 TRF1; helix-turn-helix, telomeres, DNA binding, MY 8e-19
2ckx_A83 NGTRF1, telomere binding protein TBP1; nuclear pro 3e-17
2aje_A105 Telomere repeat-binding protein; DNA-binding, Trp, 1e-15
2roh_A122 RTBP1, telomere binding protein-1; plant, nucleus, 6e-15
2juh_A121 Telomere binding protein TBP1; helix, nucleus, nuc 4e-14
1hst_A90 Histone H5; chromosomal protein; 2.60A {Gallus gal 5e-12
1uhm_A78 Histone H1, histone HHO1P; winged helix-turn-helix 5e-11
1ghc_A75 GH1; chromosomal protein; NMR {Gallus gallus} SCOP 3e-10
2rqp_A88 Heterochromatin protein 1-binding protein 3; histo 6e-10
1uss_A88 Histone H1; DNA binding protein, linker histone, D 2e-09
1ust_A93 Histone H1; DNA binding protein, linker histone, D 1e-08
2d9a_A60 B-MYB, MYB-related protein B; DNA binding, structu 2e-07
2llk_A73 Cyclin-D-binding MYB-like transcription factor 1; 4e-07
2lso_A83 Histone H1X; structural genomics, northeast struct 6e-07
1guu_A52 C-MYB, MYB proto-oncogene protein; transcription, 8e-07
2dim_A70 Cell division cycle 5-like protein; MYB_DNA-bindin 7e-06
1x58_A62 Hypothetical protein 4930532D21RIK; MUS musculus a 7e-06
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 8e-06
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 2e-05
1x41_A60 Transcriptional adaptor 2-like, isoform B; transcr 9e-06
1gvd_A52 MYB proto-oncogene protein; transcription, transcr 2e-05
2k9n_A107 MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind 2e-05
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 6e-05
2elk_A58 SPCC24B10.08C protein; hypothetical protein, struc 7e-05
4b4c_A211 Chromodomain-helicase-DNA-binding protein 1; chrom 2e-04
1gv2_A105 C-MYB, MYB proto-oncogene protein; transcription, 3e-04
1h8a_C128 AMV V-MYB, MYB transforming protein; transcription 4e-04
3zqc_A131 MYB3; transcription-DNA complex, DNA-binding prote 4e-04
3osg_A126 MYB21; transcription-DNA complex, MYB2, R2R3 domai 4e-04
>1w0u_A Telomeric repeat binding factor 2; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle, nuclear protein; 1.8A {Homo sapiens} SCOP: a.4.1.4 Length = 55 Back     alignment and structure
 Score = 84.3 bits (209), Expect = 1e-21
 Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 4/56 (7%)

Query: 5  KQKWTAEEEEALRAGVAKHGTGKWKNIQRDPEFNPFLFSRSNIDLKDKWRNMSVSA 60
          KQKWT EE E ++AGV K+G G W  I ++  F     +R+ + +KD+WR M    
Sbjct: 2  KQKWTVEESEWVKAGVQKYGEGNWAAISKNYPFV----NRTAVMIKDRWRTMKRLG 53
>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A Length = 53 Back     alignment and structure
>1vf9_A Telomeric repeat binding factor 2; MYB, helix-turn-helix, telomere, DNA binding protein; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1xg1_A 1vfc_A Length = 64 Back     alignment and structure
>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A Length = 69 Back     alignment and structure
>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A Length = 83 Back     alignment and structure
>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3 Length = 105 Back     alignment and structure
>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa} Length = 122 Back     alignment and structure
>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa} Length = 121 Back     alignment and structure
>1hst_A Histone H5; chromosomal protein; 2.60A {Gallus gallus} SCOP: a.4.5.13 Length = 90 Back     alignment and structure
>1uhm_A Histone H1, histone HHO1P; winged helix-turn-helix, linker histone, riken structural genomics/proteomics initiative, RSGI; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 Length = 78 Back     alignment and structure
>1ghc_A GH1; chromosomal protein; NMR {Gallus gallus} SCOP: a.4.5.13 Length = 75 Back     alignment and structure
>2rqp_A Heterochromatin protein 1-binding protein 3; histone H1, alternative splicing, chromosomal protein, DNA-binding, nucleus, phosphoprotein; NMR {Homo sapiens} Length = 88 Back     alignment and structure
>1uss_A Histone H1; DNA binding protein, linker histone, DNA binding domain; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 PDB: 1yqa_A Length = 88 Back     alignment and structure
>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus} Length = 60 Back     alignment and structure
>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens} Length = 73 Back     alignment and structure
>2lso_A Histone H1X; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, nuclear protein; NMR {Homo sapiens} Length = 83 Back     alignment and structure
>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A Length = 52 Back     alignment and structure
>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70 Back     alignment and structure
>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Length = 62 Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Length = 159 Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Length = 159 Back     alignment and structure
>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 60 Back     alignment and structure
>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A Length = 52 Back     alignment and structure
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A Length = 107 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe} Length = 58 Back     alignment and structure
>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens} Length = 211 Back     alignment and structure
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A Length = 105 Back     alignment and structure
>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3 Length = 128 Back     alignment and structure
>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis} Length = 131 Back     alignment and structure
>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A Length = 126 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query272
1hst_A90 Histone H5; chromosomal protein; 2.60A {Gallus gal 99.88
1uss_A88 Histone H1; DNA binding protein, linker histone, D 99.88
1uhm_A78 Histone H1, histone HHO1P; winged helix-turn-helix 99.88
1ust_A93 Histone H1; DNA binding protein, linker histone, D 99.86
2rqp_A88 Heterochromatin protein 1-binding protein 3; histo 99.84
1ghc_A75 GH1; chromosomal protein; NMR {Gallus gallus} SCOP 99.79
1x58_A62 Hypothetical protein 4930532D21RIK; MUS musculus a 99.76
2lso_A83 Histone H1X; structural genomics, northeast struct 99.62
2aje_A105 Telomere repeat-binding protein; DNA-binding, Trp, 99.71
2roh_A122 RTBP1, telomere binding protein-1; plant, nucleus, 99.68
2juh_A121 Telomere binding protein TBP1; helix, nucleus, nuc 99.67
2ckx_A83 NGTRF1, telomere binding protein TBP1; nuclear pro 99.66
3sjm_A64 Telomeric repeat-binding factor 2; human telomeric 99.66
1w0t_A53 Telomeric repeat binding factor 1; telomere, DNA-b 99.57
1ity_A69 TRF1; helix-turn-helix, telomeres, DNA binding, MY 99.54
1guu_A52 C-MYB, MYB proto-oncogene protein; transcription, 99.44
1gvd_A52 MYB proto-oncogene protein; transcription, transcr 99.41
2d9a_A60 B-MYB, MYB-related protein B; DNA binding, structu 99.41
2dim_A70 Cell division cycle 5-like protein; MYB_DNA-bindin 99.32
1x41_A60 Transcriptional adaptor 2-like, isoform B; transcr 99.3
2elk_A58 SPCC24B10.08C protein; hypothetical protein, struc 99.27
2llk_A73 Cyclin-D-binding MYB-like transcription factor 1; 99.15
1gv2_A105 C-MYB, MYB proto-oncogene protein; transcription, 99.12
2cu7_A72 KIAA1915 protein; nuclear protein, SANT domain, DN 99.11
2yum_A75 ZZZ3 protein, zinc finger ZZ-type-containing prote 99.11
3zqc_A131 MYB3; transcription-DNA complex, DNA-binding prote 99.1
2k9n_A107 MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind 99.1
3osg_A126 MYB21; transcription-DNA complex, MYB2, R2R3 domai 99.05
1h8a_C128 AMV V-MYB, MYB transforming protein; transcription 99.04
2din_A66 Cell division cycle 5-like protein; MYB_DNA-bindin 99.04
2yus_A79 SWI/SNF-related matrix-associated actin- dependent 99.02
1gv2_A105 C-MYB, MYB proto-oncogene protein; transcription, 99.01
3osg_A126 MYB21; transcription-DNA complex, MYB2, R2R3 domai 98.94
2k9n_A107 MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind 98.93
1h8a_C128 AMV V-MYB, MYB transforming protein; transcription 98.92
3zqc_A131 MYB3; transcription-DNA complex, DNA-binding prote 98.91
2cqr_A73 RSGI RUH-043, DNAJ homolog subfamily C member 1; m 98.88
2ltp_A89 Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s 98.39
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 98.86
1h89_C159 C-MYB, MYB proto-oncogene protein; transcription/D 98.74
2cjj_A93 Radialis; plant development, DNA-binding protein, 98.66
1ign_A246 Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, 98.53
2cqq_A72 RSGI RUH-037, DNAJ homolog subfamily C member 1; m 98.34
2eqr_A61 N-COR1, N-COR, nuclear receptor corepressor 1; SAN 98.28
3hm5_A93 DNA methyltransferase 1-associated protein 1; DNA 97.89
4b4c_A211 Chromodomain-helicase-DNA-binding protein 1; chrom 97.73
2iw5_B235 Protein corest, REST corepressor 1; oxidoreductase 97.71
1wgx_A73 KIAA1903 protein; MYB DNA-binding domain, human cD 97.51
2xb0_X270 Chromo domain-containing protein 1; hydrolase, DNA 97.27
1fex_A59 TRF2-interacting telomeric RAP1 protein; helix tur 97.27
4iej_A93 DNA methyltransferase 1-associated protein 1; DNA 96.98
2yqk_A63 Arginine-glutamic acid dipeptide repeats protein; 96.95
1ofc_X304 ISWI protein; nuclear protein, chromatin remodelin 96.88
2crg_A70 Metastasis associated protein MTA3; transcription 96.65
2ebi_A86 DNA binding protein GT-1; DNA-binding domain, phos 96.61
4eef_G74 F-HB80.4, designed hemagglutinin binding protein; 96.41
2xag_B482 REST corepressor 1; amine oxidase, chromatin regul 96.22
4a69_C94 Nuclear receptor corepressor 2; transcription, hyd 95.91
2y9y_A374 Imitation switch protein 1 (DEL_ATPase); transcrip 95.91
2c6y_A111 Forkhead box protein K2; transcription regulation, 94.88
2lr8_A70 CAsp8-associated protein 2; structural genomics, n 93.43
2a07_F93 Forkhead box protein P2; double-helix, swapping, h 94.36
1ug2_A95 2610100B20RIK gene product; hypothetical protein, 93.54
2hfh_A109 Genesis, HFH-2; HNF-3 homologues, winged helix pro 93.5
1vtn_C102 HNF-3/FORK head DNA-recognition motif; protein-DNA 93.43
2hdc_A97 Protein (transcription factor); structure, dyanami 93.01
4b4c_A211 Chromodomain-helicase-DNA-binding protein 1; chrom 92.98
1kq8_A100 HFH-1, hepatocyte nuclear factor 3 forkhead homolo 92.27
3g73_A142 Forkhead box protein M1; DNA-binding domain, forkh 92.08
1irz_A64 ARR10-B; helix-turn-helix, DNA binding protein; NM 91.79
3bpy_A85 FORK head domain, forkhead transcription factor FO 91.47
1ign_A246 Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, 90.92
3l2c_A110 Forkhead box protein O4; winged helix, transcripti 90.29
3coa_C117 Forkhead box protein O1; winged helix, forkhead do 90.16
2xb0_X270 Chromo domain-containing protein 1; hydrolase, DNA 86.01
1e17_A150 AFX; DNA binding domain, winged helix; NMR {Homo s 82.57
>1hst_A Histone H5; chromosomal protein; 2.60A {Gallus gallus} SCOP: a.4.5.13 Back     alignment and structure
Probab=99.88  E-value=3.7e-23  Score=161.83  Aligned_cols=74  Identities=28%  Similarity=0.429  Sum_probs=67.2

Q ss_pred             CCCCCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeecc-----ccccCCcc
Q 024081          107 ARSSAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQN-----CFKVKEDA  180 (272)
Q Consensus       107 ~~~shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK~-----sykl~~~~  180 (272)
                      .+.+||+|.+||+|||.+|+||+|||++||++||+++|+++++|+.+|+.+|++||++|.|+|++|     +|+|++..
T Consensus         3 ~~~~hP~y~~MI~eAI~~lker~GsS~~AI~KyI~~~y~~~~~~~~~l~~aLk~~v~~G~l~q~Kg~GasGsfkl~~~~   81 (90)
T 1hst_A            3 RSASHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLAKSD   81 (90)
T ss_dssp             ---CCCCHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSCCCTTHHHHHHHHHHHHHHTTSEEEECCSSCCCEEEECC--
T ss_pred             CCCCCCCHHHHHHHHHHHhccCCCCCHHHHHHHHHHHccCchhHHHHHHHHHHHHHHcCCeeeecCCCccceeecCCCc
Confidence            456899999999999999999999999999999999999977899999999999999999999998     99998654
>1uss_A Histone H1; DNA binding protein, linker histone, DNA binding domain; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 PDB: 1yqa_A Back     alignment and structure
>1uhm_A Histone H1, histone HHO1P; winged helix-turn-helix, linker histone, riken structural genomics/proteomics initiative, RSGI; NMR {Saccharomyces cerevisiae} SCOP: a.4.5.13 Back     alignment and structure
>2rqp_A Heterochromatin protein 1-binding protein 3; histone H1, alternative splicing, chromosomal protein, DNA-binding, nucleus, phosphoprotein; NMR {Homo sapiens} Back     alignment and structure
>1ghc_A GH1; chromosomal protein; NMR {Gallus gallus} SCOP: a.4.5.13 Back     alignment and structure
>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1 Back     alignment and structure
>2lso_A Histone H1X; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, nuclear protein; NMR {Homo sapiens} Back     alignment and structure
>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3 Back     alignment and structure
>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa} Back     alignment and structure
>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa} Back     alignment and structure
>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A Back     alignment and structure
>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A Back     alignment and structure
>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A Back     alignment and structure
>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A Back     alignment and structure
>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A Back     alignment and structure
>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A Back     alignment and structure
>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus} Back     alignment and structure
>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Back     alignment and structure
>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe} Back     alignment and structure
>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens} Back     alignment and structure
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A Back     alignment and structure
>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis} Back     alignment and structure
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A Back     alignment and structure
>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A Back     alignment and structure
>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3 Back     alignment and structure
>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens} Back     alignment and structure
>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A Back     alignment and structure
>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A Back     alignment and structure
>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A Back     alignment and structure
>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3 Back     alignment and structure
>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis} Back     alignment and structure
>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens} Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Back     alignment and structure
>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C Back     alignment and structure
>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3 Back     alignment and structure
>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A Back     alignment and structure
>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3hm5_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin, structural genomics consortium, SGC, activator, chromatin regulator; HET: DNA; 1.80A {Homo sapiens} Back     alignment and structure
>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens} Back     alignment and structure
>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B* Back     alignment and structure
>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3 Back     alignment and structure
>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A Back     alignment and structure
>1fex_A TRF2-interacting telomeric RAP1 protein; helix turn helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Synthetic} SCOP: a.4.1.3 Back     alignment and structure
>4iej_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin regulator, repressor, structural joint center for structural genomics; HET: DNA; 1.45A {Homo sapiens} PDB: 3hm5_A* Back     alignment and structure
>2yqk_A Arginine-glutamic acid dipeptide repeats protein; structure genomics, SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A Back     alignment and structure
>2crg_A Metastasis associated protein MTA3; transcription factor, helix turn helix, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.3 Back     alignment and structure
>2ebi_A DNA binding protein GT-1; DNA-binding domain, phosphorylation; HET: DNA; NMR {Arabidopsis thaliana} PDB: 2jmw_A* Back     alignment and structure
>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene} Back     alignment and structure
>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B* Back     alignment and structure
>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A Back     alignment and structure
>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A Back     alignment and structure
>2c6y_A Forkhead box protein K2; transcription regulation, DNA-binding domain, forkhead transcription factors, interleukin enhancer binding factor; 2.4A {Homo sapiens} SCOP: a.4.5.14 PDB: 1jxs_A 2a3s_A 2d2w_A Back     alignment and structure
>2lr8_A CAsp8-associated protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, apoptosis; NMR {Homo sapiens} Back     alignment and structure
>2a07_F Forkhead box protein P2; double-helix, swapping, homodimer, monomer, winged-helix, magnesium, transcription/DNA complex; 1.90A {Homo sapiens} SCOP: a.4.5.14 PDB: 2as5_F 2kiu_A 3qrf_F Back     alignment and structure
>1ug2_A 2610100B20RIK gene product; hypothetical protein, MYB-like DNA binding domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.4.1.3 Back     alignment and structure
>2hfh_A Genesis, HFH-2; HNF-3 homologues, winged helix protein; NMR {Rattus norvegicus} SCOP: a.4.5.14 Back     alignment and structure
>1vtn_C HNF-3/FORK head DNA-recognition motif; protein-DNA complex, double helix, transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} PDB: 1d5v_A Back     alignment and structure
>2hdc_A Protein (transcription factor); structure, dyanamics, genesis, winged helix protein, protein/DNA complex; HET: DNA; NMR {Rattus norvegicus} SCOP: a.4.5.14 Back     alignment and structure
>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens} Back     alignment and structure
>1kq8_A HFH-1, hepatocyte nuclear factor 3 forkhead homolog 1, winged; winged helix protein, structure, transcription; NMR {Rattus norvegicus} SCOP: a.4.5.14 Back     alignment and structure
>3g73_A Forkhead box protein M1; DNA-binding domain, forkhead transcription factors, FOXM1, W helix; HET: DNA; 2.21A {Homo sapiens} Back     alignment and structure
>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11 Back     alignment and structure
>3bpy_A FORK head domain, forkhead transcription factor FOXO4, DNA binding domain; forkhead BOX, winged helix; 1.87A {Homo sapiens} Back     alignment and structure
>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A Back     alignment and structure
>3l2c_A Forkhead box protein O4; winged helix, transcription-DNA COMP; 1.87A {Homo sapiens} SCOP: a.4.5.14 PDB: 3co6_C* Back     alignment and structure
>3coa_C Forkhead box protein O1; winged helix, forkhead domain, chromosomal rearrangement; HET: DNA; 2.20A {Homo sapiens} PDB: 3co7_C* 2k86_A 2uzk_A Back     alignment and structure
>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 272
d1hsta_74 a.4.5.13 (A:) Histone H5, globular domain {Chicken 3e-16
d1usta_92 a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's 1e-14
d1ghca_75 a.4.5.13 (A:) Histone H1, globular domain {Chicken 4e-14
d1ussa_88 a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's 5e-14
d1w0ta_52 a.4.1.4 (A:) DNA-binding domain of human telomeric 2e-12
d1w0ua_55 a.4.1.4 (A:) Telomeric repeat binding factor 2, TR 1e-10
d2ckxa183 a.4.1.3 (A:578-660) Telomere binding protein TBP1 1e-09
d1guua_50 a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus 6e-09
d1gvda_52 a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus 8e-06
d2cjja163 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Anti 1e-04
d1x41a147 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, T 4e-04
d2iw5b165 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Hu 7e-04
d1xc5a168 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 0.001
d1igna186 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Ba 0.002
d1gv2a247 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mou 0.002
>d1hsta_ a.4.5.13 (A:) Histone H5, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Length = 74 Back     information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H5, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 69.4 bits (170), Expect = 3e-16
 Identities = 20/61 (32%), Positives = 30/61 (49%)

Query: 110 SAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEK 169
           S P Y+ +I  AI A K   GS   +I  YI+   +V  N    +   +RRL+A   L++
Sbjct: 1   SHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQ 60

Query: 170 V 170
            
Sbjct: 61  T 61
>d1usta_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 92 Back     information, alignment and structure
>d1ghca_ a.4.5.13 (A:) Histone H1, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Length = 75 Back     information, alignment and structure
>d1ussa_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 88 Back     information, alignment and structure
>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 52 Back     information, alignment and structure
>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]} Length = 55 Back     information, alignment and structure
>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Length = 83 Back     information, alignment and structure
>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 50 Back     information, alignment and structure
>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 52 Back     information, alignment and structure
>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]} Length = 63 Back     information, alignment and structure
>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]} Length = 47 Back     information, alignment and structure
>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Length = 65 Back     information, alignment and structure
>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 68 Back     information, alignment and structure
>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86 Back     information, alignment and structure
>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 47 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 ?
Query272
d1hsta_74 Histone H5, globular domain {Chicken (Gallus gallu 99.89
d1ussa_88 Histone H1 homologue Hho1p {Baker's yeast (Sacchar 99.86
d1usta_92 Histone H1 homologue Hho1p {Baker's yeast (Sacchar 99.85
d1ghca_75 Histone H1, globular domain {Chicken (Gallus gallu 99.83
d1w0ua_55 Telomeric repeat binding factor 2, TRF2 {Human (Ho 99.68
d1w0ta_52 DNA-binding domain of human telomeric protein, hTR 99.68
d2ckxa183 Telomere binding protein TBP1 {Tobacco (Nicotiana 99.6
d1guua_50 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 99.46
d1gvda_52 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 99.46
d1gv2a247 c-Myb, DNA-binding domain {Mouse (Mus musculus) [T 99.34
d1x41a147 Transcriptional adaptor 2-like, TADA2L, isoform b 99.17
d2cqra160 DnaJ homolog subfamily C member 1 {Human (Homo sap 99.08
d1x58a149 Hypothetical protein 4930532d21rik {Mouse (Mus mus 99.04
d1igna186 DNA-binding domain of rap1 {Baker's yeast (Sacchar 99.04
d2cjja163 Radialis {Garden snapdragon (Antirrhinum majus) [T 99.01
d2cu7a165 MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960 98.96
d2iw5b165 REST corepressor 1, CoREST {Human (Homo sapiens) [ 98.78
d1xc5a168 Nuclear receptor corepressor 2 {Human (Homo sapien 98.63
d1ug2a_95 2610100b20rik gene product {Mouse (Mus musculus) [ 98.27
d2crga157 Metastasis associated protein MTA3 {Mouse (Mus mus 97.5
d1irza_64 Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId 96.82
d1ofcx2128 SLIDE domain of the nucleosome remodeling ATPase I 96.74
d2cqqa159 DnaJ homolog subfamily C member 1 {Human (Homo sap 96.68
d2fnaa173 Hypothetical protein SSO1545, C-terminal domain {S 95.82
d2a07f182 Forkhead box protein P2, FOXP2 {Human (Homo sapien 94.58
d2c6ya198 Interleukin enhancer binding factor {Human (Homo s 93.52
d2hdca_97 Genesis {Rat (Rattus norvegicus) [TaxId: 10116]} 92.58
d1d5va_94 Adipocyte-transcription factor FREAC-11 (s12, fkh- 92.55
d1fexa_59 Rap1 {Human (Homo sapiens) [TaxId: 9606]} 92.34
d3bpya185 Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]} 91.67
d1kq8a_75 HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norv 91.17
>d1hsta_ a.4.5.13 (A:) Histone H5, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Linker histone H1/H5
domain: Histone H5, globular domain
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=99.89  E-value=9.2e-24  Score=157.83  Aligned_cols=68  Identities=31%  Similarity=0.458  Sum_probs=65.9

Q ss_pred             CCCCHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhcCCCccHHHHHHHHHHhhhccCceeeec-----cccccC
Q 024081          110 SAPKYNALIFEAISALKEPNGSDVSAILSYIEQRLEVPPNFRRLLSSRLRRLVAQEKLEKVQ-----NCFKVK  177 (272)
Q Consensus       110 shp~y~~MI~EAI~~Lker~GSS~~AI~kyIe~~y~v~~nf~~~L~~~LKrlV~~GkLvkvK-----~sykl~  177 (272)
                      +||+|.+||+|||.+|+||+|||++||++||+++|.++.+|+.+|+.+|+++|++|.|+|+|     |+|||+
T Consensus         1 sHP~y~~MI~eAI~al~er~GsS~~AI~kyI~~~y~~~~~~~~~l~~aLk~~v~~G~l~q~kg~GasGsfkl~   73 (74)
T d1hsta_           1 SHPTYSEMIAAAIRAEKSRGGSSRQSIQKYIKSHYKVGHNADLQIKLSIRRLLAAGVLKQTKGVGASGSFRLA   73 (74)
T ss_dssp             CCCCHHHHHHHHHHTCCCSSCEEHHHHHHHHHHHSCCCTTHHHHHHHHHHHHHHTTSEEEECCSSCCCEEEEC
T ss_pred             CCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHcCcEEeeccCCCcceeecC
Confidence            69999999999999999999999999999999999999999999999999999999999999     499996
>d1ussa_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1usta_ a.4.5.13 (A:) Histone H1 homologue Hho1p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1ghca_ a.4.5.13 (A:) Histone H1, globular domain {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]} Back     information, alignment and structure
>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1x58a1 a.4.1.1 (A:8-56) Hypothetical protein 4930532d21rik {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]} Back     information, alignment and structure
>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1ofcx2 a.4.1.13 (X:851-978) SLIDE domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2fnaa1 a.4.5.11 (A:284-356) Hypothetical protein SSO1545, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2a07f1 a.4.5.14 (F:503-584) Forkhead box protein P2, FOXP2 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2c6ya1 a.4.5.14 (A:1-98) Interleukin enhancer binding factor {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hdca_ a.4.5.14 (A:) Genesis {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure
>d1d5va_ a.4.5.14 (A:) Adipocyte-transcription factor FREAC-11 (s12, fkh-14) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1fexa_ a.4.1.3 (A:) Rap1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d3bpya1 a.4.5.14 (A:93-177) Afx (Foxo4) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1kq8a_ a.4.5.14 (A:) HFH-1 (HNF-3 forkhead homolog-1) {Rat (Rattus norvegicus) [TaxId: 10116]} Back     information, alignment and structure