Citrus Sinensis ID: 030559

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-----
MAEGDEDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLSIPKKQSAQEAEEMEEDEESTELSASQEQATDLPQQTPQRVSFPLAKRTK
cccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHccccHHHHccccccccccccccccccEEEEEcccccc
cccccccccHHHHHHHHHHHHcccccEccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEcHHHHHHHHHHHHccccccccHHHHHHHHHHHHcccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccc
maegdedlpRDAKIVKSLLKsmgveeyeprVIHQFLEVWYRYVVDVLTDAQvysehagkttidcddIKLAVQSKvnssfsqppAREVLLELAKnrnkiplpksisapgiplppeqdtlispnyqlsipkkqSAQEAEEMEedeestelsasqeqatdlpqqtpqrvsfplakrtk
maegdedlprdaKIVKSLLksmgveeyepRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKvnssfsqppAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLSIPKKQSAQEAEEMEEDEESTELSASqeqatdlpqqtpqrvsfplakrtk
MAEGDEDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLSIPKKQsaqeaeemeedeestelsasQEQATDLPQQTPQRVSFPLAKRTK
**************VKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQ*******************************************************************************************************
*************IVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGK*TIDCDDIKLAVQS**************LLELAKNRN**************LPPEQDTLISPNYQ***************************************************
********PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQS*********PAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLSI************************************************
******DLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLS************************************PQRVS*P******
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MAEGDEDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLSIPxxxxxxxxxxxxxxxxxxxxxASQEQATDLPQQTPQRVSFPLAKRTK
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 ?
Query175 2.2.26 [Sep-21-2011]
Q16594264 Transcription initiation yes no 0.925 0.613 0.407 2e-32
Q8VI33264 Transcription initiation yes no 0.925 0.613 0.407 5e-32
Q17QQ4264 Transcription initiation yes no 0.754 0.5 0.466 8e-32
Q5BKE0264 Transcription initiation yes no 0.925 0.613 0.407 1e-31
Q6NZA9249 Transcription initiation no no 0.902 0.634 0.414 4e-31
Q62880258 Transcription initiation no no 0.685 0.465 0.466 9e-30
Q5R7P7251 Transcription initiation no no 0.914 0.637 0.396 1e-29
Q9HBM6251 Transcription initiation no no 0.914 0.637 0.396 1e-29
Q27272278 Transcription initiation yes no 0.742 0.467 0.436 3e-26
Q8SSI9137 Transcription initiation yes no 0.714 0.912 0.424 4e-23
>sp|Q16594|TAF9_HUMAN Transcription initiation factor TFIID subunit 9 OS=Homo sapiens GN=TAF9 PE=1 SV=1 Back     alignment and function desciption
 Score =  137 bits (346), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 66/162 (40%), Positives = 102/162 (62%)

Query: 6   EDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCD 65
           + +P+DA+++  +LK MG+ EYEPRVI+Q LE  +RYV  +L DA++YS HA K T+D D
Sbjct: 10  KSMPKDAQMMAQILKDMGITEYEPRVINQMLEFAFRYVTTILDDAKIYSSHAKKATVDAD 69

Query: 66  DIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQL 125
           D++LA+Q + + SF+ PP R+ LL++A+ RN+ PLP      G  LPP++  L +PNY+L
Sbjct: 70  DVRLAIQCRADQSFTSPPPRDFLLDIARQRNQTPLPLIKPYSGPRLPPDRYCLTAPNYRL 129

Query: 126 SIPKKQSAQEAEEMEEDEESTELSASQEQATDLPQQTPQRVS 167
              +K+++  A  +     S     S+     L   TPQ +S
Sbjct: 130 KSLQKKASTSAGRITVPRLSVGSVTSRPSTPTLGTPTPQTMS 171
Essential for cell viability. TAF9 and TAF9B are involved in transcriptional activation as well as repression of distinct but overlapping sets of genes. May have a role in gene regulation associated with apoptosis. TAFs are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription.
Homo sapiens (taxid: 9606)
>sp|Q8VI33|TAF9_MOUSE Transcription initiation factor TFIID subunit 9 OS=Mus musculus GN=Taf9 PE=2 SV=1 Back     alignment and function description
>sp|Q17QQ4|TAF9_BOVIN Transcription initiation factor TFIID subunit 9 OS=Bos taurus GN=TAF9 PE=2 SV=1 Back     alignment and function description
>sp|Q5BKE0|TAF9_RAT Transcription initiation factor TFIID subunit 9 OS=Rattus norvegicus GN=Taf9 PE=2 SV=1 Back     alignment and function description
>sp|Q6NZA9|TAF9B_MOUSE Transcription initiation factor TFIID subunit 9B OS=Mus musculus GN=Taf9b PE=1 SV=2 Back     alignment and function description
>sp|Q62880|TAF9B_RAT Transcription initiation factor TFIID subunit 9B OS=Rattus norvegicus GN=Taf9b PE=2 SV=2 Back     alignment and function description
>sp|Q5R7P7|TAF9B_PONAB Transcription initiation factor TFIID subunit 9B OS=Pongo abelii GN=TAF9B PE=2 SV=1 Back     alignment and function description
>sp|Q9HBM6|TAF9B_HUMAN Transcription initiation factor TFIID subunit 9B OS=Homo sapiens GN=TAF9B PE=1 SV=1 Back     alignment and function description
>sp|Q27272|TAF9_DROME Transcription initiation factor TFIID subunit 9 OS=Drosophila melanogaster GN=e(y)1 PE=1 SV=1 Back     alignment and function description
>sp|Q8SSI9|TAF9_ENCCU Transcription initiation factor TFIID subunit 9 OS=Encephalitozoon cuniculi (strain GB-M1) GN=TAF9 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query175
255560617175 protein with unknown function [Ricinus c 1.0 1.0 0.834 2e-76
224058655175 predicted protein [Populus trichocarpa] 1.0 1.0 0.828 2e-75
225442116177 PREDICTED: transcription initiation fact 1.0 0.988 0.830 2e-74
449447896179 PREDICTED: transcription initiation fact 1.0 0.977 0.762 3e-69
351727208177 uncharacterized protein LOC100306277 [Gl 0.954 0.943 0.767 1e-67
388493788183 unknown [Lotus japonicus] 0.994 0.950 0.728 6e-67
297853196182 TAFII21 [Arabidopsis lyrata subsp. lyrat 0.994 0.956 0.738 1e-65
15221048183 transcription initiation factor TFIID su 0.994 0.950 0.729 3e-65
297847844183 hypothetical protein ARALYDRAFT_474557 [ 0.994 0.950 0.723 3e-65
77416927217 unknown [Solanum tuberosum] 0.994 0.801 0.710 2e-64
>gi|255560617|ref|XP_002521322.1| protein with unknown function [Ricinus communis] gi|223539400|gb|EEF40990.1| protein with unknown function [Ricinus communis] Back     alignment and taxonomy information
 Score =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 146/175 (83%), Positives = 160/175 (91%)

Query: 1   MAEGDEDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKT 60
           MAEGDE+LPRDAKIVKSLLKSMGVE+YEPRVIHQFLE+WYRYVVDVLTDAQVYSEHAGK+
Sbjct: 1   MAEGDENLPRDAKIVKSLLKSMGVEDYEPRVIHQFLELWYRYVVDVLTDAQVYSEHAGKS 60

Query: 61  TIDCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLIS 120
            IDCDD+KLA+QSKVN SFSQPP REVLLELA+NRNKIPLPKSI+ PG+PLPPEQDTLIS
Sbjct: 61  AIDCDDVKLAIQSKVNFSFSQPPPREVLLELARNRNKIPLPKSIAGPGMPLPPEQDTLIS 120

Query: 121 PNYQLSIPKKQSAQEAEEMEEDEESTELSASQEQATDLPQQTPQRVSFPLAKRTK 175
           PNYQL+IPKKQS Q  EE EEDEES + ++SQE  TD+PQ TPQRVSFPL KR K
Sbjct: 121 PNYQLAIPKKQSVQATEETEEDEESADPNSSQEPKTDVPQGTPQRVSFPLTKRPK 175

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224058655|ref|XP_002299587.1| predicted protein [Populus trichocarpa] gi|118484348|gb|ABK94051.1| unknown [Populus trichocarpa] gi|222846845|gb|EEE84392.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|225442116|ref|XP_002273931.1| PREDICTED: transcription initiation factor TFIID subunit 9B [Vitis vinifera] gi|297742999|emb|CBI35866.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449447896|ref|XP_004141702.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Cucumis sativus] gi|449480520|ref|XP_004155919.1| PREDICTED: transcription initiation factor TFIID subunit 9-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|351727208|ref|NP_001236385.1| uncharacterized protein LOC100306277 [Glycine max] gi|255628079|gb|ACU14384.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|388493788|gb|AFK34960.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|297853196|ref|XP_002894479.1| TAFII21 [Arabidopsis lyrata subsp. lyrata] gi|297340321|gb|EFH70738.1| TAFII21 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15221048|ref|NP_175816.1| transcription initiation factor TFIID subunit D7 [Arabidopsis thaliana] gi|4587557|gb|AAD25788.1|AC006577_24 Similar to gb|U21858 transcription initiation factor TFIID 31KD subunit (TAFII32) from Homo sapiens [Arabidopsis thaliana] gi|7638157|gb|AAF65406.1|AF238327_1 putative TATA binding protein associated factor 21kDa subunit [Arabidopsis thaliana] gi|21593471|gb|AAM65438.1| transcriptional activation factor TAFII32, putative [Arabidopsis thaliana] gi|39545926|gb|AAR28026.1| TAF9 [Arabidopsis thaliana] gi|98960943|gb|ABF58955.1| At1g54140 [Arabidopsis thaliana] gi|332194933|gb|AEE33054.1| transcription initiation factor TFIID subunit D7 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|297847844|ref|XP_002891803.1| hypothetical protein ARALYDRAFT_474557 [Arabidopsis lyrata subsp. lyrata] gi|297337645|gb|EFH68062.1| hypothetical protein ARALYDRAFT_474557 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|77416927|gb|ABA81859.1| unknown [Solanum tuberosum] 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 ?
Query175
TAIR|locus:2014350183 TAFII21 "TATA binding protein 0.988 0.945 0.7 6.9e-63
DICTYBASE|DDB_G0272360 619 taf9 "TFIID subunit" [Dictyost 0.702 0.198 0.5 7.1e-31
UNIPROTKB|E2R911265 TAF9 "Uncharacterized protein" 0.925 0.611 0.388 4.9e-30
UNIPROTKB|D6RIE8198 TAF9 "Transcription initiation 0.925 0.818 0.388 4.9e-30
UNIPROTKB|Q16594264 TAF9 "Transcription initiation 0.925 0.613 0.388 4.9e-30
UNIPROTKB|Q17QQ4264 TAF9 "Transcription initiation 0.714 0.473 0.476 1.3e-29
UNIPROTKB|D6RGK3136 TAF9 "Transcription initiation 0.714 0.919 0.476 1.3e-29
UNIPROTKB|D6RIV9166 TAF9 "Transcription initiation 0.714 0.753 0.476 1.3e-29
MGI|MGI:1888697264 Taf9 "TAF9 RNA polymerase II, 0.714 0.473 0.476 1.3e-29
ZFIN|ZDB-GENE-030131-204248 taf9 "TAF9 RNA polymerase II, 0.702 0.495 0.475 1.3e-29
TAIR|locus:2014350 TAFII21 "TATA binding protein associated factor 21kDa subunit" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 126/180 (70%), Positives = 142/180 (78%)

Query:     3 EGDEDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTI 62
             EG+ED+PRDAKIVKSLLKSMGVE+YEPRVIHQFLE+WYRYVV+VLTDAQVYSEHA K  I
Sbjct:     4 EGEEDVPRDAKIVKSLLKSMGVEDYEPRVIHQFLELWYRYVVEVLTDAQVYSEHASKPNI 63

Query:    63 DCDDIKLAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPN 122
             DCDD+KLA+QSKVN SFSQPP REVLLELA +RNKIPLPKSI+ PG+PLPPEQDTL+SPN
Sbjct:    64 DCDDVKLAIQSKVNFSFSQPPPREVLLELAASRNKIPLPKSIAGPGVPLPPEQDTLLSPN 123

Query:   123 YQLSIPKK-------QXXXXXXXXXXXXXXXXXXXXQEQATDLPQQTPQRVSFPLAKRTK 175
             YQL IPKK       +                    Q+Q +DLP QTPQRVSFPL++R K
Sbjct:   124 YQLVIPKKSVSTEPEETEDDEEMTDPGQSSQEQQQQQQQTSDLPSQTPQRVSFPLSRRPK 183
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0005669 "transcription factor TFIID complex" evidence=ISS
GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA;ISS
GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA
GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA
GO:0009560 "embryo sac egg cell differentiation" evidence=RCA
DICTYBASE|DDB_G0272360 taf9 "TFIID subunit" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|E2R911 TAF9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|D6RIE8 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q16594 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q17QQ4 TAF9 "Transcription initiation factor TFIID subunit 9" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|D6RGK3 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|D6RIV9 TAF9 "Transcription initiation factor TFIID subunit 9" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1888697 Taf9 "TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-204 taf9 "TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

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

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query175
cd07979117 cd07979, TAF9, TATA Binding Protein (TBP) Associat 2e-60
pfam02291129 pfam02291, TFIID-31kDa, Transcription initiation f 1e-37
COG5094145 COG5094, TAF9, Transcription initiation factor TFI 5e-33
pfam0012575 pfam00125, Histone, Core histone H2A/H2B/H3/H4 4e-04
COG203691 COG2036, HHT1, Histones H3 and H4 [Chromatin struc 0.003
PTZ00015102 PTZ00015, PTZ00015, histone H4; Provisional 0.004
>gnl|CDD|173963 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 
 Score =  183 bits (466), Expect = 2e-60
 Identities = 70/117 (59%), Positives = 91/117 (77%)

Query: 9   PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIK 68
           PRDA+++ ++LKSMG+ EYEPRVI+Q LE  YRY  DVL DA+VYSEHAGK  ID DD+K
Sbjct: 1   PRDARVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVK 60

Query: 69  LAVQSKVNSSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQL 125
           LA+QS+V+ SF+ PP R+ LLELA+ +N IPLP    + G+ LPPE+  L +PNY+L
Sbjct: 61  LAIQSRVDYSFTSPPPRDFLLELAREKNSIPLPPIPPSCGLRLPPERYCLTAPNYRL 117

The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) which has a redundant function. Several hypotheses are proposed for TAF function such as serving as activator-binding sites, in core-promoter recognition or a role in essential catalytic activity. It has been shown that TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16 and the basal transcription factor TFIIB. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF9 is a component of TFIID in multiple organisms as well as different TBP-free TAF complexes containing the GCN5-type histone acetyltransferase. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFS and many other transcription factors. TFIID has a histone octamer-like substructure. TFIID has a histone octamer-like substructure. TAF9 is a shared subunit of both, histone acetyltransferase complex (SAGA) and TFIID complexes. TAF9 domain interacts with TAF6 to form a novel histone-like heterodimer that is structurally related to the histone H3 and H4 oligomer. Length = 117
>gnl|CDD|111209 pfam02291, TFIID-31kDa, Transcription initiation factor IID, 31kD subunit Back     alignment and domain information
>gnl|CDD|227425 COG5094, TAF9, Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4 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|185397 PTZ00015, PTZ00015, histone H4; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 175
KOG3334148 consensus Transcription initiation factor TFIID, s 100.0
PF02291129 TFIID-31kDa: Transcription initiation factor IID, 100.0
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 100.0
COG5094145 TAF9 Transcription initiation factor TFIID, subuni 100.0
PLN00035103 histone H4; Provisional 99.29
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 99.29
cd0007685 H4 Histone H4, one of the four histones, along wit 99.28
PTZ00015102 histone H4; Provisional 99.26
smart0080365 TAF TATA box binding protein associated factor. TA 99.26
smart0057677 BTP Bromodomain transcription factors and PHD doma 99.24
smart0041774 H4 Histone H4. 99.17
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 99.08
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 98.99
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 98.83
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 98.83
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 98.6
smart00428105 H3 Histone H3. 98.49
cd00074115 H2A Histone 2A; H2A is a subunit of the nucleosome 98.29
PF0296966 TAF: TATA box binding protein associated factor (T 98.28
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 98.11
PTZ00018136 histone H3; Provisional 97.83
PLN0016097 histone H3; Provisional 97.82
PLN00161135 histone H3; Provisional 97.82
PLN00121136 histone H3; Provisional 97.76
KOG3467103 consensus Histone H4 [Chromatin structure and dyna 97.74
PF15511414 CENP-T: Centromere kinetochore component CENP-T; P 97.55
KOG4336 323 consensus TBP-associated transcription factor Prod 97.54
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 97.42
KOG2389 353 consensus Predicted bromodomain transcription fact 97.2
KOG1142258 consensus Transcription initiation factor TFIID, s 96.9
PF13654509 AAA_32: AAA domain; PDB: 3K1J_B. 96.49
KOG3423176 consensus Transcription initiation factor TFIID, s 95.97
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 95.94
KOG2549 576 consensus Transcription initiation factor TFIID, s 95.94
KOG1745137 consensus Histones H3 and H4 [Chromatin structure 95.93
smart00414106 H2A Histone 2A. 95.88
PF0354051 TFIID_30kDa: Transcription initiation factor TFIID 95.62
PLN00154136 histone H2A; Provisional 95.39
PTZ00017134 histone H2A; Provisional 94.77
PTZ00463117 histone H2B; Provisional 94.19
PLN00158116 histone H2B; Provisional 94.1
cd0797892 TAF13 The TATA Binding Protein (TBP) Associated Fa 93.78
PLN00157132 histone H2A; Provisional 93.69
smart0042789 H2B Histone H2B. 93.39
TIGR00764 608 lon_rel lon-related putative ATP-dependent proteas 93.15
PLN00156139 histone H2AX; Provisional 93.04
KOG1756131 consensus Histone 2A [Chromatin structure and dyna 92.95
PLN00153129 histone H2A; Provisional 92.71
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 91.99
COG5262132 HTA1 Histone H2A [Chromatin structure and dynamics 91.92
PTZ00252134 histone H2A; Provisional 91.78
KOG0870172 consensus DNA polymerase epsilon, subunit D [Trans 91.76
PRK00411394 cdc6 cell division control protein 6; Reviewed 90.72
PRK05574340 holA DNA polymerase III subunit delta; Reviewed 89.8
COG1067 647 LonB Predicted ATP-dependent protease [Posttransla 89.8
cd08045212 TAF4 TATA Binding Protein (TBP) Associated Factor 89.38
TIGR00635305 ruvB Holliday junction DNA helicase, RuvB subunit. 89.19
TIGR03015269 pepcterm_ATPase putative secretion ATPase, PEP-CTE 89.06
TIGR01128302 holA DNA polymerase III, delta subunit. subunit ar 87.38
PRK07452326 DNA polymerase III subunit delta; Validated 87.02
PRK00080328 ruvB Holliday junction DNA helicase RuvB; Reviewed 86.95
COG5162197 Transcription initiation factor TFIID, subunit TAF 86.77
COG1466334 HolA DNA polymerase III, delta subunit [DNA replic 86.69
COG5095 450 TAF6 Transcription initiation factor TFIID, subuni 86.37
TIGR02902531 spore_lonB ATP-dependent protease LonB. Members of 86.25
PRK06585343 holA DNA polymerase III subunit delta; Reviewed 85.96
PF05236264 TAF4: Transcription initiation factor TFIID compon 85.86
KOG1744127 consensus Histone H2B [Chromatin structure and dyn 85.46
PRK05907311 hypothetical protein; Provisional 83.8
PRK08487328 DNA polymerase III subunit delta; Validated 83.51
PRK07914320 hypothetical protein; Reviewed 83.28
TIGR02397355 dnaX_nterm DNA polymerase III, subunit gamma and t 81.55
PRK12402337 replication factor C small subunit 2; Reviewed 81.26
TIGR02928365 orc1/cdc6 family replication initiation protein. M 80.5
PF1512791 DUF4565: Protein of unknown function (DUF4565) 80.46
PRK05629318 hypothetical protein; Validated 80.1
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information 
Probab=100.00  E-value=7.8e-54  Score=340.30  Aligned_cols=135  Identities=52%  Similarity=0.920  Sum_probs=128.3

Q ss_pred             CCCCC----CCCChhHHHHHHHHHhCCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhHhCCCCCCHHHHHHHHHHhhc
Q 030559            1 MAEGD----EDLPRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVN   76 (175)
Q Consensus         1 m~~~~----~~~PrDa~~I~~ILks~Gv~~yep~Vv~qLlEfayrYt~~VL~DA~~yA~HAgR~tI~~eDVrLAI~~r~~   76 (175)
                      |++|+    +..||||++|+.||+++||++|||+|++||||||||||+.||+||+.||+||+|.+|++|||||||+++++
T Consensus         1 m~sg~~~~~~~~pkDa~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~   80 (148)
T KOG3334|consen    1 MSSGEKSGTKGVPKDARVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVD   80 (148)
T ss_pred             CCCcccCcccCCcHHHHHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhc
Confidence            66666    89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCcHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCceee-CCCCCCcch
Q 030559           77 SSFSQPPAREVLLELAKNRNKIPLPKSISAPGIPLPPEQDTLISPNYQLS-IPKKQSAQE  135 (175)
Q Consensus        77 ~~f~~pppre~LlelA~e~N~~PLP~v~~~~GirLPpe~~cLt~~Ny~l~-~p~~~~~~~  135 (175)
                      ++|++||||++|+++|.+||++|||.+..+||+||||++||||++||.++ .+|+...+.
T Consensus        81 ~sf~~pPpRe~lL~lA~~rN~~pLp~i~~~~g~rLPpdryclt~~n~~l~~~~kk~~~~~  140 (148)
T KOG3334|consen   81 HSFTPPPPREFLLELAAERNSKPLPQIRAGPGLRLPPDRYCLTQPNYVLKNLQKKEMQQA  140 (148)
T ss_pred             cccCCCCchHHHHHHHHhhccCCCCcccCCCCccCChhHHHhcCccceeecccccccccC
Confidence            99999999999999999999999999999999999999999999999999 555554444

>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
>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
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>PLN00035 histone H4; Provisional Back     alignment and domain information
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics] 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
>PTZ00015 histone H4; Provisional Back     alignment and domain information
>smart00803 TAF TATA box binding protein associated factor Back     alignment and domain information
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins Back     alignment and domain information
>smart00417 H4 Histone H4 Back     alignment and domain information
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C 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
>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
>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
>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
>smart00428 H3 Histone H3 Back     alignment and domain information
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome 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
>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
>PTZ00018 histone H3; Provisional Back     alignment and domain information
>PLN00160 histone H3; Provisional Back     alignment and domain information
>PLN00161 histone H3; Provisional Back     alignment and domain information
>PLN00121 histone H3; Provisional Back     alignment and domain information
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics] 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
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription] 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
>KOG2389 consensus Predicted bromodomain transcription factor [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
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B Back     alignment and domain information
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription] 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
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics] Back     alignment and domain information
>smart00414 H2A Histone 2A Back     alignment and domain information
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors Back     alignment and domain information
>PLN00154 histone H2A; Provisional Back     alignment and domain information
>PTZ00017 histone H2A; Provisional Back     alignment and domain information
>PTZ00463 histone H2B; Provisional Back     alignment and domain information
>PLN00158 histone H2B; Provisional Back     alignment and domain information
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex Back     alignment and domain information
>PLN00157 histone H2A; Provisional Back     alignment and domain information
>smart00427 H2B Histone H2B Back     alignment and domain information
>TIGR00764 lon_rel lon-related putative ATP-dependent protease Back     alignment and domain information
>PLN00156 histone H2AX; Provisional Back     alignment and domain information
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics] Back     alignment and domain information
>PLN00153 histone H2A; Provisional Back     alignment and domain information
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription] Back     alignment and domain information
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics] Back     alignment and domain information
>PTZ00252 histone H2A; Provisional Back     alignment and domain information
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription] Back     alignment and domain information
>PRK00411 cdc6 cell division control protein 6; Reviewed Back     alignment and domain information
>PRK05574 holA DNA polymerase III subunit delta; Reviewed Back     alignment and domain information
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones] 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
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit Back     alignment and domain information
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily Back     alignment and domain information
>TIGR01128 holA DNA polymerase III, delta subunit Back     alignment and domain information
>PRK07452 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed Back     alignment and domain information
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] Back     alignment and domain information
>TIGR02902 spore_lonB ATP-dependent protease LonB Back     alignment and domain information
>PRK06585 holA DNA polymerase III subunit delta; Reviewed 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
>PRK05907 hypothetical protein; Provisional Back     alignment and domain information
>PRK08487 DNA polymerase III subunit delta; Validated Back     alignment and domain information
>PRK07914 hypothetical protein; Reviewed Back     alignment and domain information
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau Back     alignment and domain information
>PRK12402 replication factor C small subunit 2; Reviewed Back     alignment and domain information
>TIGR02928 orc1/cdc6 family replication initiation protein Back     alignment and domain information
>PF15127 DUF4565: Protein of unknown function (DUF4565) Back     alignment and domain information
>PRK05629 hypothetical protein; Validated Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query175
1taf_A68 Drosophila Tbp Associated Factors Dtafii42DTAFII62 1e-16
>pdb|1TAF|A Chain A, Drosophila Tbp Associated Factors Dtafii42DTAFII62 HETEROTETRAMER Length = 68 Back     alignment and structure 
Iteration: 1

 Score = 82.4 bits (202), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 34/64 (53%), Positives = 50/64 (78%)
Query: 9  PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIK 68
          P+DA+++ S+LK + V+EYEPRV++Q LE  +RYV  +L DA+VY+ HA K TID DD++
Sbjct: 1  PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVR 60
Query: 69 LAVQ 72
          LA +
Sbjct: 61 LATE 64

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query175
1taf_A68 TFIID TBP associated factor 42; transcription init 3e-32
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 1e-08
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 6e-08
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 9e-06
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 4e-05
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 1e-04
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 3e-04
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 3e-04
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 6e-04
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 7e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-04
>1taf_A TFIID TBP associated factor 42; transcription initiation, histone fold, complex (TWO transcr factors); 2.00A {Drosophila melanogaster} SCOP: a.22.1.3 Length = 68 Back     alignment and structure
 Score =  109 bits (273), Expect = 3e-32
 Identities = 34/68 (50%), Positives = 52/68 (76%)

Query: 9  PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIK 68
          P+DA+++ S+LK + V+EYEPRV++Q LE  +RYV  +L DA+VY+ HA K TID DD++
Sbjct: 1  PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVR 60

Query: 69 LAVQSKVN 76
          LA +  ++
Sbjct: 61 LATEVTLD 68
>3v9r_A MHF1, uncharacterized protein YOL086W-A; histone fold, fanconi anemia, DNA repair, DNA BI protein; 2.40A {Saccharomyces cerevisiae} Length = 90 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 Length = 113 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 Length = 111 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 ... Length = 103 Back     alignment and structure
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} Length = 107 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 Length = 84 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 Length = 102 Back     alignment and structure
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A Length = 140 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
>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

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query175
1taf_A68 TFIID TBP associated factor 42; transcription init 99.96
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 99.65
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 99.6
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 99.54
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 99.54
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 99.49
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 99.39
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 99.33
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 99.32
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 99.3
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 99.3
1taf_B70 TFIID TBP associated factor 62; transcription init 99.24
1f1e_A154 Histone fold protein; archaeal histone protein, DN 99.03
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 98.97
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 98.97
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 98.94
1f1e_A154 Histone fold protein; archaeal histone protein, DN 98.83
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 98.83
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 98.72
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 98.66
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 98.55
3r45_A156 Histone H3-like centromeric protein A; histone fol 98.55
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 98.53
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 98.51
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 98.51
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 98.4
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 98.37
1tzy_A129 Histone H2A-IV; histone-fold, tetramer-dimer-dimer 98.35
2f8n_K149 Histone H2A type 1; nucleosome, NCP, macroh2A, his 98.3
1id3_C131 Histone H2A.1; nucleosome core particle, chromatin 98.29
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 98.23
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 98.16
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 98.13
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 98.12
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 98.08
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 97.89
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 97.57
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 97.52
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 97.49
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 97.31
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 97.18
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 97.07
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 96.31
3uk6_A368 RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding 95.05
3bos_A242 Putative DNA replication factor; P-loop containing 93.55
2r44_A331 Uncharacterized protein; putative ATPase, structur 92.89
1g8p_A350 Magnesium-chelatase 38 kDa subunit; parallel beta 92.85
2c9o_A456 RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP- 92.49
2keb_A101 DNA polymerase subunit alpha B; DNA polymerase alp 92.16
4dra_E84 Centromere protein X; DNA binding complex, DNA dam 92.06
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 91.92
3k1j_A 604 LON protease, ATP-dependent protease LON; ATP-bind 89.99
2v1u_A387 Cell division control protein 6 homolog; DNA repli 89.53
1in4_A334 RUVB, holliday junction DNA helicase RUVB; AAA+-cl 89.33
2chg_A226 Replication factor C small subunit; DNA-binding pr 88.91
1jr3_D343 DNA polymerase III, delta subunit; processivity, p 86.43
2qby_A386 CDC6 homolog 1, cell division control protein 6 ho 86.01
1njg_A250 DNA polymerase III subunit gamma; rossman-like fol 84.77
2qby_B384 CDC6 homolog 3, cell division control protein 6 ho 83.82
1sxj_D353 Activator 1 41 kDa subunit; clamp loader, processi 83.29
1fnn_A389 CDC6P, cell division control protein 6; ORC1, AAA 83.19
3ksy_A 1049 SOS-1, SON of sevenless homolog 1; RAS, RAS activa 83.04
1h3o_A75 Transcription initiation factor TFIID 135 kDa subu 82.68
3pfi_A338 Holliday junction ATP-dependent DNA helicase RUVB; 82.68
>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
Probab=99.96  E-value=6.7e-30  Score=180.21  Aligned_cols=68  Identities=50%  Similarity=0.909  Sum_probs=66.3

Q ss_pred             ChhHHHHHHHHHhCCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhHhCCCCCCHHHHHHHHHHhhc
Q 030559            9 PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVN   76 (175)
Q Consensus         9 PrDa~~I~~ILks~Gv~~yep~Vv~qLlEfayrYt~~VL~DA~~yA~HAgR~tI~~eDVrLAI~~r~~   76 (175)
                      |||+++|++||++|||++|||+|++||+||+|||+.+||+||..||+||||+||+++||||||++|++
T Consensus         1 Prda~~i~~iLk~~G~~~~~~~v~~~L~e~~~ry~~~il~dA~~~a~HAgrktv~~eDVkLAi~~~~~   68 (68)
T 1taf_A            1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTLD   68 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC-
T ss_pred             CchhHHHHHHHHHCCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhccC
Confidence            89999999999999999999999999999999999999999999999999999999999999999874
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 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
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} 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
>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
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A 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
>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
>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
>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
>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
>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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} 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
>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
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} 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
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>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
>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
>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
>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
>2nqb_C Histone H2A; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_C* 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
>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
>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
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {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
>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
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D* 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
>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
>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
>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
>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
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D* Back     alignment and structure
>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A Back     alignment and structure
>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406} Back     alignment and structure
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G Back     alignment and structure
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* Back     alignment and structure
>2keb_A DNA polymerase subunit alpha B; DNA polymerase alpha, DNA replication, nucleus, phosphoprote binding protein; HET: DNA; NMR {Homo sapiens} 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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} Back     alignment and structure
>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus} Back     alignment and structure
>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Back     alignment and structure
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A* Back     alignment and structure
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus} Back     alignment and structure
>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A* Back     alignment and structure
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Back     alignment and structure
>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A* Back     alignment and structure
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Back     alignment and structure
>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Back     alignment and structure
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Back     alignment and structure
>3ksy_A SOS-1, SON of sevenless homolog 1; RAS, RAS activator, disease mutation, guanine-nucleotide releasing factor, signaling protein; 3.18A {Homo sapiens} PDB: 1xd4_A 1xdv_A 1q9c_A Back     alignment and structure
>1h3o_A Transcription initiation factor TFIID 135 kDa subunit; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3 Back     alignment and structure
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} 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 175
d1tafa_68 a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila mel 2e-34
d2huec182 a.22.1.1 (C:20-101) Histone H4 {African clawed fro 9e-07
d1htaa_68 a.22.1.2 (A:) Archaeal histone {Archaeon Methanoth 7e-04
d1ku5a_66 a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococc 0.002
d1f1ea_151 a.22.1.2 (A:) Archaeal histone {Archaeon Methanopy 0.003
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 68 Back     information, alignment and structure

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score =  114 bits (286), Expect = 2e-34
 Identities = 34/68 (50%), Positives = 52/68 (76%)

Query: 9  PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIK 68
          P+DA+++ S+LK + V+EYEPRV++Q LE  +RYV  +L DA+VY+ HA K TID DD++
Sbjct: 1  PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVR 60

Query: 69 LAVQSKVN 76
          LA +  ++
Sbjct: 61 LATEVTLD 68
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} Length = 82 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
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Length = 151 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 ?
Query175
d1tafa_68 TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta 99.97
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 99.15
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 98.96
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 98.84
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.75
d1q9ca_172 Histone domain of Son of sevenless protein {Human 98.51
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 98.5
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 98.4
d1tafb_70 TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta 97.93
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 97.78
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 97.62
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 97.41
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 97.36
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 96.98
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 96.95
d1u35c1106 macro-H2A.1, histone domain {Human (Homo sapiens) 96.49
d1tzya_106 Histone H2A {Chicken (Gallus gallus), erythrocytes 96.41
d1f66c_103 Histone H2A {Human (Homo sapiens), variant H2A.Z [ 96.24
d1tzyb_92 Histone H2B {Chicken (Gallus gallus), erythrocytes 95.73
d1w5sa2287 CDC6-like protein APE0152, N-terminal domain {Aero 95.07
d1fnna2276 CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T 94.99
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 92.54
d1ixsb2239 Holliday junction helicase RuvB {Thermus thermophi 92.25
d1sxjc2227 Replication factor C3 {Baker's yeast (Saccharomyce 91.11
d1sxjd2237 Replication factor C2 {Baker's yeast (Saccharomyce 82.31
d1in4a2238 Holliday junction helicase RuvB {Thermotoga mariti 82.1
>d1tafa_ a.22.1.3 (A:) TAF(II)42 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Back     information, alignment and structure
class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)42
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.97  E-value=2.4e-32  Score=191.15  Aligned_cols=68  Identities=50%  Similarity=0.909  Sum_probs=66.4

Q ss_pred             ChhHHHHHHHHHhCCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHhHhCCCCCCHHHHHHHHHHhhc
Q 030559            9 PRDAKIVKSLLKSMGVEEYEPRVIHQFLEVWYRYVVDVLTDAQVYSEHAGKTTIDCDDIKLAVQSKVN   76 (175)
Q Consensus         9 PrDa~~I~~ILks~Gv~~yep~Vv~qLlEfayrYt~~VL~DA~~yA~HAgR~tI~~eDVrLAI~~r~~   76 (175)
                      |||+++|+.||++|||++|||+|++|||||+|||+++||+||+.||+||||++|+++||||||++|++
T Consensus         1 PrDa~~i~~iL~~~GV~~yeprV~~qlLef~yRYtt~VL~DA~vys~HA~k~~id~dDVkLAi~~r~d   68 (68)
T d1tafa_           1 PKDAQVIMSILKELNVQEYEPRVVNQLLEFTFRYVTSILDDAKVYANHARKKTIDLDDVRLATEVTLD   68 (68)
T ss_dssp             CHHHHHHHHHHHHTTCCCBCTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHTC-
T ss_pred             CcHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhccC
Confidence            89999999999999999999999999999999999999999999999999999999999999999975
>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]} 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
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} 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
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} Back     information, alignment and structure
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} 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
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>d1jfib_ a.22.1.3 (B:) Negative cofactor 2, NC2, beta chain {Human (Homo sapiens) [TaxId: 9606]} 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
>d1u35c1 a.22.1.1 (C:814-919) macro-H2A.1, histone domain {Human (Homo sapiens) [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
>d1f66c_ a.22.1.1 (C:) Histone H2A {Human (Homo sapiens), variant H2A.Z [TaxId: 9606]} Back     information, alignment and structure
>d1tzyb_ a.22.1.1 (B:) Histone H2B {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} Back     information, alignment and structure
>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 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
>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure