Citrus Sinensis ID: 031980

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-------15
MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQPW
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccccc
ccccHHHHcHcccccccccccccHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccHHEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEcHHHHHHHHHHHcccccc
MARTKHMARRSSRLQAavkatpptsspgtsrqrrseagegtptaqrkrqrlrpGTKALREIRRFQKSVDLLIPRMSFIREVRTityrvappdvnrwtPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARrlggkgqpw
martkhmarrssrlqaavkatpptsspgtsrqrrseagegtptaqrkrqrlrpgtkalreirrfqksvdlliprmsfirevrtityrvappdvnrWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELarrlggkgqpw
MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQPW
***********************************************************EIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELA**********
MARTK***************************************************ALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK****
****************************************************PGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQPW
************************************************QRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGG*****
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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
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MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQPW
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 ?
Query149 2.2.26 [Sep-21-2011]
Q8RVQ9178 Histone H3-like centromer yes no 0.946 0.792 0.615 5e-44
Q7RXR3155 Histone H3-like centromer N/A no 0.872 0.838 0.511 1e-29
Q59LN9211 Histone H3-like centromer N/A no 0.704 0.497 0.555 5e-27
P15512136 Histone H3.3 OS=Tetrahyme N/A no 0.899 0.985 0.468 1e-24
P41353136 Histone H3.3 OS=Tetrahyme N/A no 0.899 0.985 0.468 1e-24
P69150136 Histone H3 OS=Tetrahymena N/A no 0.899 0.985 0.468 2e-24
P69149136 Histone H3 OS=Tetrahymena N/A no 0.899 0.985 0.468 2e-24
Q9Y812120 Histone H3-like centromer yes no 0.724 0.9 0.544 3e-24
Q22RG7136 Histone H3.4 OS=Tetrahyme N/A no 0.899 0.985 0.462 3e-24
Q402E2136 Histone H3.3a OS=Lilium l N/A no 0.885 0.970 0.489 3e-24
>sp|Q8RVQ9|HTR12_ARATH Histone H3-like centromeric protein HTR12 OS=Arabidopsis thaliana GN=HTR12 PE=1 SV=3 Back     alignment and function desciption
 Score =  176 bits (445), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 88/143 (61%), Positives = 109/143 (76%), Gaps = 2/143 (1%)

Query: 9   RRSSRLQAAVKATPPTSSPGTSRQRRSE-AGEGTP-TAQRKRQRLRPGTKALREIRRFQK 66
           RR        + T PT+SP T  +R ++ + +  P  +Q+K  R RPGT AL+EIR FQK
Sbjct: 36  RRGGEGGDNTQQTNPTTSPATGTRRGAKRSRQAMPRGSQKKSYRYRPGTVALKEIRHFQK 95

Query: 67  SVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHA 126
             +LLIP  SFIREVR+IT+ +APP +NRWT EAL+ALQEAAED+LV LF D+MLCAIHA
Sbjct: 96  QTNLLIPAASFIREVRSITHMLAPPQINRWTAEALVALQEAAEDYLVGLFSDSMLCAIHA 155

Query: 127 KRVTLMKKDFELARRLGGKGQPW 149
           +RVTLM+KDFELARRLGGKG+PW
Sbjct: 156 RRVTLMRKDFELARRLGGKGRPW 178
Histone H3-like variant which exclusively replaces conventional H3 in the nucleosome core of centromeric chromatin at the inner plate of the kinetochore. Required for recruitment and assembly of kinetochore proteins, mitotic progression and chromosome segregation. May serve as an epigenetic mark that propagates centromere identity through replication and cell division.
Arabidopsis thaliana (taxid: 3702)
>sp|Q7RXR3|CENPA_NEUCR Histone H3-like centromeric protein cse-4 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=cse-4 PE=3 SV=1 Back     alignment and function description
>sp|Q59LN9|CENPA_CANAL Histone H3-like centromeric protein CSE4 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=CSE4 PE=3 SV=1 Back     alignment and function description
>sp|P15512|H33_TETPY Histone H3.3 OS=Tetrahymena pyriformis PE=1 SV=2 Back     alignment and function description
>sp|P41353|H33_TETTS Histone H3.3 OS=Tetrahymena thermophila (strain SB210) GN=HHT3 PE=1 SV=2 Back     alignment and function description
>sp|P69150|H31_TETTH Histone H3 OS=Tetrahymena thermophila GN=HHT1 PE=1 SV=2 Back     alignment and function description
>sp|P69149|H31_TETPY Histone H3 OS=Tetrahymena pyriformis PE=1 SV=2 Back     alignment and function description
>sp|Q9Y812|CENPA_SCHPO Histone H3-like centromeric protein cnp1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cnp1 PE=1 SV=1 Back     alignment and function description
>sp|Q22RG7|H34_TETTS Histone H3.4 OS=Tetrahymena thermophila (strain SB210) GN=HHT4 PE=2 SV=1 Back     alignment and function description
>sp|Q402E2|H33A_LILLO Histone H3.3a OS=Lilium longiflorum GN=MPH3 PE=2 SV=3 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 ?
Query149
134152507175 putative centromeric histone H3-like pro 1.0 0.851 0.542 2e-44
33146144174 histone H3 like protein [Turritis glabra 1.0 0.856 0.568 2e-44
91178263166 histone H3 [Arabidopsis lyrata subsp. pe 1.0 0.897 0.590 3e-44
91178255172 histone H3 [Arabidopsis lyrata subsp. pe 1.0 0.866 0.569 9e-44
91178261172 histone H3 [Arabidopsis lyrata subsp. pe 1.0 0.866 0.569 9e-44
134152513175 centromeric histone H3-like protein-2 [C 1.0 0.851 0.548 2e-43
134152531180 centromeric histone H3-like protein_1 [L 1.0 0.827 0.538 2e-43
51103319176 centromeric histone [Arabidopsis lyrata] 1.0 0.846 0.556 2e-43
91178265176 histone H3 [Arabidopsis lyrata subsp. pe 1.0 0.846 0.556 2e-43
91179092173 histone H3 [Arabidopsis lyrata subsp. pe 1.0 0.861 0.554 2e-43
>gi|134152507|dbj|BAF49719.1| putative centromeric histone H3-like protein_1 [Arabis hirsuta] Back     alignment and taxonomy information
 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 95/175 (54%), Positives = 116/175 (66%), Gaps = 26/175 (14%)

Query: 1   MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRS-----EAGEGTP------------- 42
           MARTKH ARR      A  ++ P + P T+  RR+     +A + TP             
Sbjct: 1   MARTKHFARRGQNRTDANVSSSPAAGPSTTPARRASEDGDDAQQTTPATSPATGSKNSNG 60

Query: 43  --------TAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVN 94
                   ++Q+K  R RPGT ALREIR+FQKS  LLIP  SFIREV+ ITY  APP + 
Sbjct: 61  GAKRTMPQSSQKKPHRYRPGTAALREIRKFQKSTKLLIPAASFIREVKDITYTYAPPQIT 120

Query: 95  RWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQPW 149
           RWT EAL+A+QEAAED+LV LF D+MLCA+HA+RVTLM+KDFELARRLGGKG+PW
Sbjct: 121 RWTAEALVAIQEAAEDYLVGLFSDSMLCAVHARRVTLMRKDFELARRLGGKGRPW 175

Source: Arabis hirsuta

Species: Arabis hirsuta

Genus: Arabis

Family: Brassicaceae

Order: Brassicales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|33146144|dbj|BAC79432.1| histone H3 like protein [Turritis glabra] Back     alignment and taxonomy information
>gi|91178263|gb|ABE27638.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178271|gb|ABE27642.1| histone H3 [Arabidopsis lyrata subsp. petraea] Back     alignment and taxonomy information
>gi|91178255|gb|ABE27634.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178259|gb|ABE27636.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178267|gb|ABE27640.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178277|gb|ABE27645.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178279|gb|ABE27646.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178287|gb|ABE27650.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178289|gb|ABE27651.1| histone H3 [Arabidopsis lyrata subsp. petraea] Back     alignment and taxonomy information
>gi|91178261|gb|ABE27637.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178275|gb|ABE27644.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178281|gb|ABE27647.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178291|gb|ABE27652.1| histone H3 [Arabidopsis lyrata subsp. petraea] Back     alignment and taxonomy information
>gi|134152513|dbj|BAF49722.1| centromeric histone H3-like protein-2 [Cardamine flexuosa] Back     alignment and taxonomy information
>gi|134152531|dbj|BAF49731.1| centromeric histone H3-like protein_1 [Lepidium virginicum] Back     alignment and taxonomy information
>gi|51103319|gb|AAT96392.1| centromeric histone [Arabidopsis lyrata] Back     alignment and taxonomy information
>gi|91178265|gb|ABE27639.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178269|gb|ABE27641.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178273|gb|ABE27643.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178293|gb|ABE27653.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178295|gb|ABE27654.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178297|gb|ABE27655.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91178299|gb|ABE27656.1| histone H3 [Arabidopsis lyrata subsp. petraea] Back     alignment and taxonomy information
>gi|91179092|gb|ABE27602.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179096|gb|ABE27604.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179114|gb|ABE27613.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179116|gb|ABE27614.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179118|gb|ABE27615.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179120|gb|ABE27616.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179122|gb|ABE27617.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179124|gb|ABE27618.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179126|gb|ABE27619.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179128|gb|ABE27620.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179138|gb|ABE27625.1| histone H3 [Arabidopsis lyrata subsp. petraea] gi|91179140|gb|ABE27626.1| histone H3 [Arabidopsis lyrata subsp. petraea] 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 ?
Query149
TAIR|locus:2035252178 HTR12 [Arabidopsis thaliana (t 0.865 0.724 0.656 8.4e-42
ASPGD|ASPL0000001462191 AN6554 [Emericella nidulans (t 0.865 0.675 0.481 3.2e-26
CGD|CAL0006066211 CSE4 [Candida albicans (taxid: 0.832 0.587 0.5 4e-26
UNIPROTKB|Q59LN9211 CSE4 "Histone H3-like centrome 0.832 0.587 0.5 4e-26
ZFIN|ZDB-GENE-050626-58136 zgc:113983 "zgc:113983" [Danio 0.899 0.985 0.489 1.2e-24
POMBASE|SPBC1105.17120 cnp1 "centromere-specific hist 0.724 0.9 0.562 5.3e-24
FB|FBgn0051613136 His3:CG31613 "His3:CG31613" [D 0.899 0.985 0.482 8.7e-24
FB|FBgn0053803136 His3:CG33803 "His3:CG33803" [D 0.899 0.985 0.482 8.7e-24
FB|FBgn0053806136 His3:CG33806 "His3:CG33806" [D 0.899 0.985 0.482 8.7e-24
FB|FBgn0053809136 His3:CG33809 "His3:CG33809" [D 0.899 0.985 0.482 8.7e-24
TAIR|locus:2035252 HTR12 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 86/131 (65%), Positives = 105/131 (80%)

Query:    21 TPPTSSPGTSRQRRSEAG-EGTPT-AQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFI 78
             T PT+SP T  +R ++   +  P  +Q+K  R RPGT AL+EIR FQK  +LLIP  SFI
Sbjct:    48 TNPTTSPATGTRRGAKRSRQAMPRGSQKKSYRYRPGTVALKEIRHFQKQTNLLIPAASFI 107

Query:    79 REVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFEL 138
             REVR+IT+ +APP +NRWT EAL+ALQEAAED+LV LF D+MLCAIHA+RVTLM+KDFEL
Sbjct:   108 REVRSITHMLAPPQINRWTAEALVALQEAAEDYLVGLFSDSMLCAIHARRVTLMRKDFEL 167

Query:   139 ARRLGGKGQPW 149
             ARRLGGKG+PW
Sbjct:   168 ARRLGGKGRPW 178
GO:0000786 "nucleosome" evidence=IEA
GO:0003677 "DNA binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IDA
GO:0006334 "nucleosome assembly" evidence=IEA
GO:0000775 "chromosome, centromeric region" evidence=IDA
GO:0005515 "protein binding" evidence=IPI
GO:0009567 "double fertilization forming a zygote and endosperm" evidence=IEP
GO:0000785 "chromatin" evidence=IDA
GO:0007126 "meiosis" evidence=IMP
GO:0051301 "cell division" evidence=IMP
GO:0051307 "meiotic chromosome separation" evidence=IMP
GO:0000911 "cytokinesis by cell plate formation" evidence=RCA
GO:0006270 "DNA replication initiation" evidence=RCA
GO:0006275 "regulation of DNA replication" evidence=RCA
GO:0006346 "methylation-dependent chromatin silencing" evidence=RCA
GO:0008283 "cell proliferation" evidence=RCA
GO:0009909 "regulation of flower development" evidence=RCA
GO:0010389 "regulation of G2/M transition of mitotic cell cycle" evidence=RCA
GO:0016458 "gene silencing" evidence=RCA
GO:0031048 "chromatin silencing by small RNA" evidence=RCA
GO:0034968 "histone lysine methylation" evidence=RCA
GO:0048451 "petal formation" evidence=RCA
GO:0048453 "sepal formation" evidence=RCA
GO:0051567 "histone H3-K9 methylation" evidence=RCA
GO:0051726 "regulation of cell cycle" evidence=RCA
ASPGD|ASPL0000001462 AN6554 [Emericella nidulans (taxid:162425)] Back     alignment and assigned GO terms
CGD|CAL0006066 CSE4 [Candida albicans (taxid:5476)] Back     alignment and assigned GO terms
UNIPROTKB|Q59LN9 CSE4 "Histone H3-like centromeric protein CSE4" [Candida albicans SC5314 (taxid:237561)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-050626-58 zgc:113983 "zgc:113983" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
POMBASE|SPBC1105.17 cnp1 "centromere-specific histone H3 CENP-A" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms
FB|FBgn0051613 His3:CG31613 "His3:CG31613" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
FB|FBgn0053803 His3:CG33803 "His3:CG33803" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
FB|FBgn0053806 His3:CG33806 "His3:CG33806" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
FB|FBgn0053809 His3:CG33809 "His3:CG33809" [Drosophila melanogaster (taxid:7227)] 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) ?
Q71DI3H32_HUMANNo assigned EC number0.48270.89930.9852yesno
Q7RXR3CENPA_NEUCRNo assigned EC number0.51140.87240.8387N/Ano
Q8RVQ9HTR12_ARATHNo assigned EC number0.61530.94630.7921yesno
Q4QRF4H32_DANRENo assigned EC number0.48270.89930.9852yesno
O15819H33A_DICDINo assigned EC number0.46200.91940.9856yesno
P02299H3_DROMENo assigned EC number0.48270.89930.9852yesno
P84227H32_BOVINNo assigned EC number0.48270.89930.9852yesno
P84228H32_MOUSENo assigned EC number0.48270.89930.9852yesno
Q9Y812CENPA_SCHPONo assigned EC number0.54460.72480.9yesno
P84229H32_CHICKNo assigned EC number0.48270.89930.9852yesno
Q6CER9CENPA_YARLINo assigned EC number0.44660.93950.9333yesno

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 ?
Query149
smart00428105 smart00428, H3, Histone H3 8e-34
PLN00161135 PLN00161, PLN00161, histone H3; Provisional 2e-32
PTZ00018136 PTZ00018, PTZ00018, histone H3; Provisional 3e-30
PLN00121136 PLN00121, PLN00121, histone H3; Provisional 2e-25
PLN0016097 PLN00160, PLN00160, histone H3; Provisional 4e-25
COG203691 COG2036, HHT1, Histones H3 and H4 [Chromatin struc 1e-18
pfam0012575 pfam00125, Histone, Core histone H2A/H2B/H3/H4 1e-16
>gnl|CDD|128705 smart00428, H3, Histone H3 Back     alignment and domain information 
 Score =  114 bits (286), Expect = 8e-34
 Identities = 54/99 (54%), Positives = 66/99 (66%)

Query: 46  RKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQ 105
            K +R RPG  ALREIR++QKS DLLI +  F R VR I  +       R+   A++ALQ
Sbjct: 4   TKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQ 63

Query: 106 EAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGG 144
           EAAE +LV LF D  L AIHAKRVT+M KD +LARR+ G
Sbjct: 64  EAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRG 102

Length = 105
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional Back     alignment and domain information
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional Back     alignment and domain information
>gnl|CDD|177733 PLN00121, PLN00121, histone H3; Provisional Back     alignment and domain information
>gnl|CDD|165727 PLN00160, PLN00160, histone H3; Provisional Back     alignment and domain information
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 149
PLN00161135 histone H3; Provisional 100.0
PTZ00018136 histone H3; Provisional 100.0
PLN00121136 histone H3; Provisional 100.0
KOG1745137 consensus Histones H3 and H4 [Chromatin structure 100.0
smart00428105 H3 Histone H3. 100.0
PLN0016097 histone H3; Provisional 100.0
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 99.95
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 99.83
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 99.36
cd0007685 H4 Histone H4, one of the four histones, along wit 99.12
PLN00035103 histone H4; Provisional 99.06
PTZ00015102 histone H4; Provisional 99.06
smart0080365 TAF TATA box binding protein associated factor. TA 98.98
smart0041774 H4 Histone H4. 98.89
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 98.59
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 98.55
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 98.26
smart0057677 BTP Bromodomain transcription factors and PHD doma 98.18
cd00074115 H2A Histone 2A; H2A is a subunit of the nucleosome 97.91
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 97.89
KOG0870172 consensus DNA polymerase epsilon, subunit D [Trans 97.7
PF0296966 TAF: TATA box binding protein associated factor (T 97.64
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 97.62
PF15511414 CENP-T: Centromere kinetochore component CENP-T; P 97.59
PF02291129 TFIID-31kDa: Transcription initiation factor IID, 97.44
KOG1142258 consensus Transcription initiation factor TFIID, s 97.08
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 96.31
KOG3334148 consensus Transcription initiation factor TFIID, s 95.36
KOG3467103 consensus Histone H4 [Chromatin structure and dyna 94.92
smart00414106 H2A Histone 2A. 94.61
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 94.03
PTZ00017134 histone H2A; Provisional 92.64
PLN00158116 histone H2B; Provisional 92.41
smart0042789 H2B Histone H2B. 92.34
PTZ00463117 histone H2B; Provisional 91.78
PLN00154136 histone H2A; Provisional 91.45
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 90.77
KOG0871156 consensus Class 2 transcription repressor NC2, bet 90.21
PLN00156139 histone H2AX; Provisional 90.2
PLN00157132 histone H2A; Provisional 89.76
COG5262132 HTA1 Histone H2A [Chromatin structure and dynamics 89.63
PLN00153129 histone H2A; Provisional 89.12
COG5094145 TAF9 Transcription initiation factor TFIID, subuni 87.26
cd08045212 TAF4 TATA Binding Protein (TBP) Associated Factor 87.06
PTZ00252134 histone H2A; Provisional 86.7
KOG2549 576 consensus Transcription initiation factor TFIID, s 86.51
PF05236 264 TAF4: Transcription initiation factor TFIID compon 86.01
KOG1744127 consensus Histone H2B [Chromatin structure and dyn 83.66
KOG2389 353 consensus Predicted bromodomain transcription fact 83.58
COG5150148 Class 2 transcription repressor NC2, beta subunit 82.64
>PLN00161 histone H3; Provisional Back     alignment and domain information 
Probab=100.00  E-value=1.7e-58  Score=353.62  Aligned_cols=130  Identities=50%  Similarity=0.721  Sum_probs=117.9

Q ss_pred             CCCcccccccccCcccccccCCCCCCCCcchhhhhhcCCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHH
Q 031980            1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE   80 (149)
Q Consensus         1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL   80 (149)
                      ||||||+ +|+++|+.|.+++..               +..+++++++||||||||||+|||+||+||+|||||+||+||
T Consensus         1 mar~k~~-~~~~~~~~~~~~~~~---------------~~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RL   64 (135)
T PLN00161          1 MARRLQG-KRFRKGKKPQKEASG---------------VTRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARL   64 (135)
T ss_pred             CCccccc-ccccCCCCCcccCCC---------------CCCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHH
Confidence            9999999 777888888776641               012267899999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCCC
Q 031980           81 VRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKGQ  147 (149)
Q Consensus        81 VrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~~  147 (149)
                      ||||++++ ..+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+||++|||++.
T Consensus        65 VREI~~~~-~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~~  130 (135)
T PLN00161         65 VREISNEM-LREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPIY  130 (135)
T ss_pred             HHHHHHhc-CCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhccccc
Confidence            99999994 3468999999999999999999999999999999999999999999999999999854

>PTZ00018 histone H3; Provisional Back     alignment and domain information
>PLN00121 histone H3; Provisional Back     alignment and domain information
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>smart00428 H3 Histone H3 Back     alignment and domain information
>PLN00160 histone H3; Provisional Back     alignment and domain information
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ] Back     alignment and domain information
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution Back     alignment and domain information
>PLN00035 histone H4; Provisional Back     alignment and domain information
>PTZ00015 histone H4; Provisional Back     alignment and domain information
>smart00803 TAF TATA box binding protein associated factor Back     alignment and domain information
>smart00417 H4 Histone H4 Back     alignment and domain information
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin Back     alignment and domain information
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C Back     alignment and domain information
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins Back     alignment and domain information
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome Back     alignment and domain information
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription] Back     alignment and domain information
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex Back     alignment and domain information
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [] Back     alignment and domain information
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T Back     alignment and domain information
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [] Back     alignment and domain information
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO) Back     alignment and domain information
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics] Back     alignment and domain information
>smart00414 H2A Histone 2A Back     alignment and domain information
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription] Back     alignment and domain information
>PTZ00017 histone H2A; Provisional Back     alignment and domain information
>PLN00158 histone H2B; Provisional Back     alignment and domain information
>smart00427 H2B Histone H2B Back     alignment and domain information
>PTZ00463 histone H2B; Provisional Back     alignment and domain information
>PLN00154 histone H2A; Provisional Back     alignment and domain information
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18) Back     alignment and domain information
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] Back     alignment and domain information
>PLN00156 histone H2AX; Provisional Back     alignment and domain information
>PLN00157 histone H2A; Provisional Back     alignment and domain information
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics] Back     alignment and domain information
>PLN00153 histone H2A; Provisional Back     alignment and domain information
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information
>PTZ00252 histone H2A; Provisional Back     alignment and domain information
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site Back     alignment and domain information
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics] Back     alignment and domain information
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription] Back     alignment and domain information
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [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 ?
Query149
3av1_A139 The Human Nucleosome Structure Containing The Histo 1e-24
2hio_C136 Histone Octamer (Chicken), Chromosomal Protein Leng 2e-24
3afa_A139 The Human Nucleosome Structure Length = 139 2e-24
2cv5_A136 Crystal Structure Of Human Nucleosome Core Particle 2e-24
3azf_A139 Crystal Structure Of Human Nucleosome Core Particle 2e-24
3lel_A136 Structural Insight Into The Sequence-Dependence Of 2e-24
1f66_A136 2.6 A Crystal Structure Of A Nucleosome Core Partic 2e-24
3aze_A139 Crystal Structure Of Human Nucleosome Core Particle 2e-24
3azh_A139 Crystal Structure Of Human Nucleosome Core Particle 4e-24
3azg_A139 Crystal Structure Of Human Nucleosome Core Particle 4e-24
3ayw_A139 Crystal Structure Of Human Nucleosome Core Particle 4e-24
3av2_A139 The Human Nucleosome Structure Containing The Histo 6e-24
1p3b_A135 Crystallographic Studies Of Nucleosome Core Particl 7e-24
4hga_B136 Structure Of The Variant Histone H3.3-H4 Heterodime 7e-24
2io5_B135 Crystal Structure Of The Cia- Histone H3-H4 Complex 8e-24
3a6n_A139 The Nucleosome Containing A Testis-Specific Histone 1e-23
1kx3_A135 X-Ray Structure Of The Nucleosome Core Particle, Nc 1e-23
4h9s_A135 Complex Structure 6 Of DaxxH3.3(SUB7)H4 Length = 13 1e-23
1p3a_A135 Crystallographic Studies Of Nucleosome Core Particl 2e-23
1p3k_A135 Crystallographic Studies Of Nucleosome Core Particl 3e-23
1p3m_A135 Crystallographic Studies Of Nucleosome Core Particl 3e-23
3kxb_A135 Structural Characterization Of H3k56q Nucleosomes A 3e-23
1p3l_A135 Crystallographic Studies Of Nucleosome Core Particl 3e-23
4h9o_A135 Complex Structure 2 Of DaxxH3.3(SUB5,G90M)H4 Length 4e-23
1p34_A135 Crystallographic Studies Of Nucleosome Core Particl 4e-23
1zla_A135 X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus L 6e-23
1m18_A135 Ligand Binding Alters The Structure And Dynamics Of 1e-22
4h9n_A135 Complex Structure 1 Of DaxxH3.3(SUB5)H4 Length = 13 2e-22
3c1c_A135 The Effect Of H3 K79 Dimethylation And H4 K20 Trime 2e-22
1aoi_A116 Complex Between Nucleosome Core Particle (H3,H4,H2a 3e-22
3kwq_A98 Structural Characterization Of H3k56q Nucleosomes A 3e-21
1hio_C93 Histone Octamer (Chicken), Chromosomal Protein, Alp 3e-21
1id3_A135 Crystal Structure Of The Yeast Nucleosome Core Part 5e-21
2yfv_A100 The Heterotrimeric Complex Of Kluyveromyces Lactis 7e-18
4h9p_A135 Complex Structure 3 Of DaxxH3.3(SUB5,G90A)H4 Length 2e-17
2yfw_A92 Heterotetramer Structure Of Kluyveromyces Lactis Cs 2e-17
3an2_A143 The Structure Of The Centromeric Nucleosome Contain 3e-17
3r45_A156 Structure Of A Cenp-A-Histone H4 Heterodimer In Com 3e-17
3nqu_A140 Crystal Structure Of Partially Trypsinized (Cenp-AH 3e-17
2l5a_A 235 Structural Basis For Recognition Of Centromere Spec 3e-13
4eo5_B76 Yeast Asf1 Bound To H3H4G94P MUTANT Length = 76 3e-12
3nqj_A82 Crystal Structure Of (Cenp-AH4)2 HETEROTETRAMER Len 3e-12
2hue_B77 Structure Of The H3-h4 Chaperone Asf1 Bound To Hist 3e-12
2ly8_A121 The Budding Yeast Chaperone Scm3 Recognizes The Par 2e-04
>pdb|3AV1|A Chain A, The Human Nucleosome Structure Containing The Histone Variant H3.2 Length = 139 Back     alignment and structure 
Iteration: 1

 Score =  108 bits (269), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 70/145 (48%), Positives = 89/145 (61%), Gaps = 11/145 (7%)
Query: 1   MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALRE 60
           MARTK  AR+S+  +A      P     T   R+S    G     +K  R RPGT ALRE
Sbjct: 4   MARTKQTARKSTGGKA------PRKQLATKAARKSAPATG---GVKKPHRYRPGTVALRE 54
Query: 61  IRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAM 120
           IRR+QKS +LLI ++ F R VR I       D+ R+   A++ALQEA+E +LV LF D  
Sbjct: 55  IRRYQKSTELLIRKLPFQRLVREIAQDF-KTDL-RFQSSAVMALQEASEAYLVGLFEDTN 112
Query: 121 LCAIHAKRVTLMKKDFELARRLGGK 145
           LCAIHAKRVT+M KD +LARR+ G+
Sbjct: 113 LCAIHAKRVTIMPKDIQLARRIRGE 137
>pdb|2HIO|C Chain C, Histone Octamer (Chicken), Chromosomal Protein Length = 136 Back     alignment and structure
>pdb|3AFA|A Chain A, The Human Nucleosome Structure Length = 139 Back     alignment and structure
>pdb|2CV5|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Length = 136 Back     alignment and structure
>pdb|3AZF|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Containing H3k79q Mutation Length = 139 Back     alignment and structure
>pdb|3LEL|A Chain A, Structural Insight Into The Sequence-Dependence Of Nucleosom Positioning Length = 136 Back     alignment and structure
>pdb|1F66|A Chain A, 2.6 A Crystal Structure Of A Nucleosome Core Particle Containing The Variant Histone H2a.Z Length = 136 Back     alignment and structure
>pdb|3AZE|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Containing H3k64q Mutation Length = 139 Back     alignment and structure
>pdb|3AZH|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Containing H3k122q Mutation Length = 139 Back     alignment and structure
>pdb|3AZG|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Containing H3k115q Mutation Length = 139 Back     alignment and structure
>pdb|3AYW|A Chain A, Crystal Structure Of Human Nucleosome Core Particle Containing H3k56q Mutation Length = 139 Back     alignment and structure
>pdb|3AV2|A Chain A, The Human Nucleosome Structure Containing The Histone Variant H3.3 Length = 139 Back     alignment and structure
>pdb|1P3B|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|4HGA|B Chain B, Structure Of The Variant Histone H3.3-H4 Heterodimer In Complex With Its Chaperone Daxx Length = 136 Back     alignment and structure
>pdb|2IO5|B Chain B, Crystal Structure Of The Cia- Histone H3-H4 Complex Length = 135 Back     alignment and structure
>pdb|3A6N|A Chain A, The Nucleosome Containing A Testis-Specific Histone Variant, Human H3t Length = 139 Back     alignment and structure
>pdb|1KX3|A Chain A, X-Ray Structure Of The Nucleosome Core Particle, Ncp146, At 2.0 A Resolution Length = 135 Back     alignment and structure
>pdb|4H9S|A Chain A, Complex Structure 6 Of DaxxH3.3(SUB7)H4 Length = 135 Back     alignment and structure
>pdb|1P3A|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|1P3K|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|1P3M|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|3KXB|A Chain A, Structural Characterization Of H3k56q Nucleosomes And Nucleosomal Arrays Length = 135 Back     alignment and structure
>pdb|1P3L|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|4H9O|A Chain A, Complex Structure 2 Of DaxxH3.3(SUB5,G90M)H4 Length = 135 Back     alignment and structure
>pdb|1P34|A Chain A, Crystallographic Studies Of Nucleosome Core Particles Containing Histone 'sin' Mutants Length = 135 Back     alignment and structure
>pdb|1ZLA|A Chain A, X-Ray Structure Of A Kaposi's Sarcoma Herpesvirus Lana Peptide Bound To The Nucleosomal Core Length = 135 Back     alignment and structure
>pdb|1M18|A Chain A, Ligand Binding Alters The Structure And Dynamics Of Nucleosomal Dna Length = 135 Back     alignment and structure
>pdb|4H9N|A Chain A, Complex Structure 1 Of DaxxH3.3(SUB5)H4 Length = 135 Back     alignment and structure
>pdb|3C1C|A Chain A, The Effect Of H3 K79 Dimethylation And H4 K20 Trimethylation On Nucleosome And Chromatin Structure Length = 135 Back     alignment and structure
>pdb|1AOI|A Chain A, Complex Between Nucleosome Core Particle (H3,H4,H2a,H2b) And 146 Bp Long Dna Fragment Length = 116 Back     alignment and structure
>pdb|3KWQ|A Chain A, Structural Characterization Of H3k56q Nucleosomes And Nucleo Arrays Length = 98 Back     alignment and structure
>pdb|1HIO|C Chain C, Histone Octamer (Chicken), Chromosomal Protein, Alpha Carbons Only Length = 93 Back     alignment and structure
>pdb|1ID3|A Chain A, Crystal Structure Of The Yeast Nucleosome Core Particle Reveals Fundamental Differences In Inter-Nucleosome Interactions Length = 135 Back     alignment and structure
>pdb|2YFV|A Chain A, The Heterotrimeric Complex Of Kluyveromyces Lactis Scm3, Cse4 And H4 Length = 100 Back     alignment and structure
>pdb|4H9P|A Chain A, Complex Structure 3 Of DaxxH3.3(SUB5,G90A)H4 Length = 135 Back     alignment and structure
>pdb|2YFW|A Chain A, Heterotetramer Structure Of Kluyveromyces Lactis Cse4,H4 Length = 92 Back     alignment and structure
>pdb|3AN2|A Chain A, The Structure Of The Centromeric Nucleosome Containing Cenp-A Length = 143 Back     alignment and structure
>pdb|3R45|A Chain A, Structure Of A Cenp-A-Histone H4 Heterodimer In Complex With Chaperone Hjurp Length = 156 Back     alignment and structure
>pdb|3NQU|A Chain A, Crystal Structure Of Partially Trypsinized (Cenp-AH4)2 HETEROTETRAMER Length = 140 Back     alignment and structure
>pdb|2L5A|A Chain A, Structural Basis For Recognition Of Centromere Specific Histone H3 Variant By Nonhistone Scm3 Length = 235 Back     alignment and structure
>pdb|4EO5|B Chain B, Yeast Asf1 Bound To H3H4G94P MUTANT Length = 76 Back     alignment and structure
>pdb|3NQJ|A Chain A, Crystal Structure Of (Cenp-AH4)2 HETEROTETRAMER Length = 82 Back     alignment and structure
>pdb|2HUE|B Chain B, Structure Of The H3-h4 Chaperone Asf1 Bound To Histones H3 And H4 Length = 77 Back     alignment and structure
>pdb|2LY8|A Chain A, The Budding Yeast Chaperone Scm3 Recognizes The Partially Unfolded Dimer Of The Centromere-specific Cse4/h4 Histone Variant Length = 121 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 ?
Query149
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 2e-26
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 3e-23
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 4e-22
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 1e-21
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 3e-21
3r45_A156 Histone H3-like centromeric protein A; histone fol 2e-20
2l5a_A 235 Histone H3-like centromeric protein CSE4, protein 7e-18
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 1e-05
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 2e-05
>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A Length = 100 Back     alignment and structure
 Score = 94.9 bits (235), Expect = 2e-26
 Identities = 45/99 (45%), Positives = 65/99 (65%), Gaps = 1/99 (1%)

Query: 45  QRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAP-PDVNRWTPEALIA 103
           + +  R +P   AL EIR++Q+S DLLI RM F R V+ +T +     +  RW   A++A
Sbjct: 1   KARGTRYKPTDLALAEIRKYQRSTDLLISRMPFARLVKEVTDQFTTESEPLRWQSMAIMA 60

Query: 104 LQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRL 142
           LQEA+E +LV L     L A+HAKR+T+M+KD +LARR+
Sbjct: 61  LQEASEAYLVGLLEHTNLLALHAKRITIMRKDMQLARRI 99
>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A 3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A* 1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ... Length = 136 Back     alignment and structure
>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A Length = 140 Back     alignment and structure
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens} Length = 82 Back     alignment and structure
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} Length = 77 Back     alignment and structure
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens} Length = 156 Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Length = 235 Back     alignment and structure
>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A Length = 68 Back     alignment and structure
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Length = 70 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query149
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 100.0
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 100.0
3r45_A156 Histone H3-like centromeric protein A; histone fol 100.0
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 100.0
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 100.0
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 100.0
2l5a_A 235 Histone H3-like centromeric protein CSE4, protein 100.0
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 99.95
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 99.84
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 99.74
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 99.66
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 99.11
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 99.11
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 99.11
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 99.07
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 99.01
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.0
1taf_B70 TFIID TBP associated factor 62; transcription init 98.89
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 98.88
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 98.87
1taf_A68 TFIID TBP associated factor 42; transcription init 98.86
1f1e_A154 Histone fold protein; archaeal histone protein, DN 98.85
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 98.83
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 98.8
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 98.68
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 98.67
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 98.64
2r10_A 361 Chromatin structure-remodeling complex protein RSC 98.57
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 98.46
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 98.26
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 98.04
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 97.99
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 97.98
1tzy_A129 Histone H2A-IV; histone-fold, tetramer-dimer-dimer 97.96
2f8n_K149 Histone H2A type 1; nucleosome, NCP, macroh2A, his 97.89
1id3_C131 Histone H2A.1; nucleosome core particle, chromatin 97.85
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 97.82
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 97.82
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 97.73
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 97.65
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 97.49
2x4w_B26 Histone H3.2; transcription, metal-binding, zinc-f 97.49
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 97.44
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 97.38
2jss_A 192 Chimera of histone H2B.1 and histone H2A.Z; histon 96.69
3a1b_A159 DNA (cytosine-5)-methyltransferase 3A, histone H3; 93.63
4dra_E84 Centromere protein X; DNA binding complex, DNA dam 87.92
3b0b_C81 CENP-X, centromere protein X; histone fold, DNA bi 86.8
>1tzy_C Histone H3; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_C 1hq3_C 2aro_C 2f8n_A 2hio_C 3av1_A 3lel_A 3afa_A 3azi_A 3azj_A 3azk_A 3azl_A 3azm_A 3azn_A 2cv5_A* 1u35_A* 2nqb_A 2io5_B 2pyo_A* 3c9k_C ... Back     alignment and structure
Probab=100.00  E-value=2.1e-63  Score=380.69  Aligned_cols=135  Identities=49%  Similarity=0.689  Sum_probs=91.7

Q ss_pred             CCCcccccccccCcccccccCCCCCCCCcchhhhhhcCCCCCCccCCcccCCCCchhhHHHHhhhhcccccCCcchHHHH
Q 031980            1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE   80 (149)
Q Consensus         1 MartK~~a~k~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL   80 (149)
                      ||||||+|+||+||++|++|++        +|+++++.|++ ++++++||||||++||+|||+||+||+|||||+||+||
T Consensus         1 MARtk~tarkstggkaprk~l~--------~k~a~k~~p~~-~~~kk~~r~rpgt~alrEIr~yQkst~lLIpk~PF~RL   71 (136)
T 1tzy_C            1 MARTKQTARKSTGGKAPRKQLA--------TKAARKSAPAT-GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRL   71 (136)
T ss_dssp             --------------------------------------------------CCHHHHHHHHHHHHHHCCSCCSCHHHHHHH
T ss_pred             CCCCccccccCCCCCCCCcccc--------ccccccCCCCC-CCCCCCCCCCCchhHHHHHHHhhcchhhhhccchHHHH
Confidence            9999999999999999999987        45545444443 78999999999999999999999999999999999999


Q ss_pred             HHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccccccccHHHHHHHccCC
Q 031980           81 VRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGKG  146 (149)
Q Consensus        81 VrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvTi~~kDiqLa~rirg~~  146 (149)
                      ||||+++  +..++|||++|++|||||+|+|||+||||+|+||+||||||||++|||||++|||+.
T Consensus        72 VREI~~~--~~~~~R~q~~Al~aLQeaaEayLv~Lfeda~l~A~HAkRvTi~~kDiqLa~rirg~~  135 (136)
T 1tzy_C           72 VREIAQD--FKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER  135 (136)
T ss_dssp             HHHHHHH--HCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHTCC
T ss_pred             HHHHHHH--hhhhhcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccCcHHhHHHHHHHhCcC
Confidence            9999999  456899999999999999999999999999999999999999999999999999984
>2yfv_A Histone H3-like centromeric protein CSE4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140} PDB: 2yfw_A Back     alignment and structure
>3r45_A Histone H3-like centromeric protein A; histone fold, centromere, CENP-A, histone chaperone, hjurp; 2.60A {Homo sapiens} Back     alignment and structure
>3nqu_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.50A {Homo sapiens} PDB: 3an2_A Back     alignment and structure
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens} Back     alignment and structure
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A Back     alignment and structure
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 Back     alignment and structure
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ... Back     alignment and structure
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} Back     alignment and structure
>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Back     alignment and structure
>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B Back     alignment and structure
>3b0c_T CENP-T, centromere protein T; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_T* 3vh5_T 3vh6_T Back     alignment and structure
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2 Back     alignment and structure
>1taf_B TFIID TBP associated factor 62; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Back     alignment and structure
>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W Back     alignment and structure
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Back     alignment and structure
>1f1e_A Histone fold protein; archaeal histone protein, DNA binding protein; HET: MSE; 1.37A {Methanopyrus kandleri} SCOP: a.22.1.2 Back     alignment and structure
>4dra_A Centromere protein S; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_A Back     alignment and structure
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} Back     alignment and structure
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Back     alignment and structure
>2byk_B Chrac-14; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_B Back     alignment and structure
>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>2r10_A Chromatin structure-remodeling complex protein RSC4, linker, histone H3; bromodomain, remodeler, acetylation, transcription; HET: ALY; 2.20A {Saccharomyces cerevisiae} PDB: 2r0v_A* Back     alignment and structure
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>4g92_C HAPE; transcription factor, nucleosome, minor groove binding, CCAA complex, histone fold motif, specific binding to the ccaat- nucleus; HET: DNA; 1.80A {Aspergillus nidulans} PDB: 4g91_C* Back     alignment and structure
>1jfi_A Transcription regulator NC2 alpha chain; histone, H2A/H2B, tata-DNA, transcription initiation, NC2, negative cofactor, structural genomics, PSI; 2.62A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>2f8n_G Core histone macro-H2A.1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Homo sapiens} SCOP: a.22.1.1 PDB: 1u35_C Back     alignment and structure
>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C* Back     alignment and structure
>1tzy_A Histone H2A-IV; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_A 1hq3_A 2aro_A 2hio_A 3c9k_A 3azg_C 3a6n_C 3an2_C 3av1_C 3av2_C 3ayw_C 3aze_C 3azf_C 3afa_C 3azh_C 3azi_C 3azj_C 3azk_C 3azl_C 3azm_C ... Back     alignment and structure
>2f8n_K Histone H2A type 1; nucleosome, NCP, macroh2A, histone variant, chromatin, X- RAY structure, crystallography, structural protein/DNA complex; 2.90A {Mus musculus} SCOP: a.22.1.1 Back     alignment and structure
>1id3_C Histone H2A.1; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1 Back     alignment and structure
>1f66_C Histone H2A.Z; nucleosome, chromatin, histone variant, protein DNA interaction, nucleoprotein, supercoiled DNA, complex (nucleosome core/DNA); 2.60A {Homo sapiens} SCOP: a.22.1.1 Back     alignment and structure
>2l5a_A Histone H3-like centromeric protein CSE4, protein histone H4; A single chain of CSE4+SCM3+H4, fusion protein; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1 Back     alignment and structure
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D* Back     alignment and structure
>2byk_A Chrac-16; nucleosome sliding, histone fold, DNA-binding protein; 2.4A {Drosophila melanogaster} SCOP: a.22.1.3 PDB: 2bym_A Back     alignment and structure
>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D 3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D 3azj_D 3azk_D 3azl_D 3azm_D ... Back     alignment and structure
>2jss_A Chimera of histone H2B.1 and histone H2A.Z; histone/chaperone complex, intrinsically unfolded protein, chaperone/structural protein complex; NMR {Saccharomyces cerevisiae} SCOP: a.22.1.1 a.22.1.1 Back     alignment and structure
>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger, histone binding, chromosomal protein, DNA damag repair, DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens} PDB: 3a1a_A* Back     alignment and structure
>4dra_E Centromere protein X; DNA binding complex, DNA damage repair, histone-fold, DNA BI protein; 2.41A {Homo sapiens} PDB: 4drb_J Back     alignment and structure
>3b0b_C CENP-X, centromere protein X; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} PDB: 3vh5_D 3vh6_D 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 149
d1tzyc_95 a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), 2e-36
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 3e-09
d1htaa_68 a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth 1e-04
d1ku5a_66 a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc 1e-04
d1n1ja_87 a.22.1.3 (A:) Nuclear transcription factor Y subun 0.001
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Length = 95 Back     information, alignment and structure

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

 Score =  119 bits (299), Expect = 2e-36
 Identities = 53/94 (56%), Positives = 66/94 (70%), Gaps = 2/94 (2%)

Query: 52  RPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDF 111
           RPGT ALREIRR+QKS +LLI ++ F R VR I          R+   A++ALQEA+E +
Sbjct: 2   RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTD--LRFQSSAVMALQEASEAY 59

Query: 112 LVNLFGDAMLCAIHAKRVTLMKKDFELARRLGGK 145
           LV LF D  LCAIHAKRVT+M KD +LARR+ G+
Sbjct: 60  LVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 93
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151 Back     information, alignment and structure
>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Length = 68 Back     information, alignment and structure
>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Length = 66 Back     information, alignment and structure
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Length = 87 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 ?
Query149
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 100.0
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 99.34
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 99.2
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 99.1
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 98.79
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 98.78
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.69
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 98.44
d1q9ca_172 Histone domain of Son of sevenless protein {Human 98.36
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 98.3
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 98.23
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 98.17
d1tafb_70 TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta 97.62
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 97.56
d1tafa_68 TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta 97.53
d1tzyb_92 Histone H2B {Chicken (Gallus gallus), erythrocytes 96.19
d1u35c1106 macro-H2A.1, histone domain {Human (Homo sapiens) 95.83
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 95.69
d1f66c_103 Histone H2A {Human (Homo sapiens), variant H2A.Z [ 95.56
d1tzya_106 Histone H2A {Chicken (Gallus gallus), erythrocytes 95.24
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H3
species: Chicken (Gallus gallus), erythrocytes [TaxId: 9031]

Probab=100.00  E-value=4.1e-50  Score=289.29  Aligned_cols=94  Identities=56%  Similarity=0.833  Sum_probs=91.4

Q ss_pred             CCCCchhhHHHHhhhhcccccCCcchHHHHHHHHhhhcCCCCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCccc
Q 031980           51 LRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQEAAEDFLVNLFGDAMLCAIHAKRVT  130 (149)
Q Consensus        51 ~rpgt~alrEIr~yQkst~lLIpk~PF~RLVrEI~~~~~~~~~~Rfq~~Al~aLQeAaE~yLv~Lfeda~lcA~HAkRvT  130 (149)
                      ||||++||+|||+||+||+|||||+||+||||||+++  +.+++|||++||++||||+|+|||+||||+|+||+|+||||
T Consensus         1 ~rpGt~ALrEIRk~Qkst~lLIpk~pF~RLVRei~~~--~~~~~r~~~~Al~aLQea~E~yLv~lfeda~~~a~HakRvT   78 (95)
T d1tzyc_           1 YRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQD--FKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT   78 (95)
T ss_dssp             CCHHHHHHHHHHHHHHCCSCCSCHHHHHHHHHHHHHH--HCTTCEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSE
T ss_pred             CCCchHHHHHHHHHhCCcccccccccHHHHHHHHHHh--cCCCCEeeHHHHHHHHHHHHHHHHHHHHHhHHHHHhcCCCc
Confidence            8999999999999999999999999999999999999  45689999999999999999999999999999999999999


Q ss_pred             cccccHHHHHHHccCC
Q 031980          131 LMKKDFELARRLGGKG  146 (149)
Q Consensus       131 i~~kDiqLa~rirg~~  146 (149)
                      ||++||+||++|||+.
T Consensus        79 l~~kD~~LarrirG~r   94 (95)
T d1tzyc_          79 IMPKDIQLARRIRGER   94 (95)
T ss_dssp             ECHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHHHhccC
Confidence            9999999999999984
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]} Back     information, alignment and structure
>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]} Back     information, alignment and structure
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Back     information, alignment and structure
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1q9ca_ a.22.1.3 (A:) Histone domain of Son of sevenless protein {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bykb1 a.22.1.3 (B:11-99) Chrac-14 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1jfia_ a.22.1.3 (A:) Negative cofactor 2, NC2, alpha chain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2byka1 a.22.1.3 (A:29-100) Chrac-16 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]} Back     information, alignment and structure
>d1tzya_ a.22.1.1 (A:) Histone H2A {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure