Citrus Sinensis ID: 033028

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-------13
MSNPSTGQSSKSKAGSSQPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEVDEEKLASVE
ccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccc
cccccccccccccccccccccccccHcccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccc
msnpstgqsskskagssqpyettsfkrkrgvFQKDLQHMmygfgddpnplpeTVALVEDIVVEYVTDLAHKAqdigskggklsVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEVDEEKLASVE
msnpstgqsskskagssqpyettsfkrkrgVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHkaqdigskggklsVEDFLYLIRKDLPKLNRCTELLSMQEELKQArkafevdeeklasve
MSNPstgqsskskagssqPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEVDEEKLASVE
******************************VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELL************************
*********************************KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKA***********VEDFLYLIRKDLPKLNRCTELLSMQEELKQ****************
**************************RKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAF***********
****************************RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEV***K*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSNPSTGQSSKSKAGSSQPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTExxxxxxxxxxxxxxxxxxxxxLASVE
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 ?
Query129 2.2.26 [Sep-21-2011]
Q5R9W6124 Transcription initiation yes no 0.713 0.741 0.553 9e-24
P61216124 Transcription initiation yes no 0.713 0.741 0.553 9e-24
Q15543124 Transcription initiation yes no 0.713 0.741 0.553 9e-24
Q148M7124 Transcription initiation yes no 0.713 0.741 0.553 9e-24
Q54CN8106 Transcription initiation yes no 0.736 0.896 0.5 8e-21
O60076111 Transcription initiation yes no 0.751 0.873 0.360 5e-15
P11747167 Transcription initiation yes no 0.736 0.568 0.362 1e-11
O14311 307 SAGA complex subunit spt3 no no 0.658 0.276 0.344 3e-09
O75486 399 Transcription initiation no no 0.875 0.283 0.338 1e-08
O13472 328 Protein SPT3 OS=Kluyverom no no 0.604 0.237 0.337 6e-06
>sp|Q5R9W6|TAF13_PONAB Transcription initiation factor TFIID subunit 13 OS=Pongo abelii GN=TAF13 PE=2 SV=1 Back     alignment and function desciption
 Score =  108 bits (270), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 52/94 (55%), Positives = 73/94 (77%), Gaps = 2/94 (2%)

Query: 26  KRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVE 85
           KRKR +F K+L+ MMYGFGDD NP  E+V ++ED+V+E++T++ HKA  IG + G++ VE
Sbjct: 27  KRKR-LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSIG-RQGRVQVE 84

Query: 86  DFLYLIRKDLPKLNRCTELLSMQEELKQARKAFE 119
           D ++LIRKD  K  R  +LL+M EELK+ARKAF+
Sbjct: 85  DIVFLIRKDPRKFARVKDLLTMNEELKRARKAFD 118
TFIID beta-specific TAFII.
Pongo abelii (taxid: 9601)
>sp|P61216|TAF13_MOUSE Transcription initiation factor TFIID subunit 13 OS=Mus musculus GN=Taf13 PE=2 SV=1 Back     alignment and function description
>sp|Q15543|TAF13_HUMAN Transcription initiation factor TFIID subunit 13 OS=Homo sapiens GN=TAF13 PE=1 SV=1 Back     alignment and function description
>sp|Q148M7|TAF13_BOVIN Transcription initiation factor TFIID subunit 13 OS=Bos taurus GN=TAF13 PE=2 SV=1 Back     alignment and function description
>sp|Q54CN8|TAF13_DICDI Transcription initiation factor TFIID subunit 13 OS=Dictyostelium discoideum GN=taf13 PE=3 SV=1 Back     alignment and function description
>sp|O60076|TAF13_SCHPO Transcription initiation factor TFIID subunit 13 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=taf13 PE=3 SV=3 Back     alignment and function description
>sp|P11747|TAF13_YEAST Transcription initiation factor TFIID subunit 13 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TAF13 PE=1 SV=2 Back     alignment and function description
>sp|O14311|SPT3_SCHPO SAGA complex subunit spt3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=spt3 PE=1 SV=2 Back     alignment and function description
>sp|O75486|SUPT3_HUMAN Transcription initiation protein SPT3 homolog OS=Homo sapiens GN=SUPT3H PE=1 SV=2 Back     alignment and function description
>sp|O13472|SPT3_KLULA Protein SPT3 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=SPT3 PE=3 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 ?
Query129
255548497128 Transcription initiation factor TFIID su 0.992 1.0 0.922 1e-60
315937242128 transcription initiation factor TFIID su 0.992 1.0 0.914 1e-60
358248250136 uncharacterized protein LOC100796504 [Gl 0.984 0.933 0.828 6e-54
388515967136 unknown [Lotus japonicus] 0.984 0.933 0.812 8e-54
356534862136 PREDICTED: transcription initiation fact 0.984 0.933 0.820 2e-53
390098822130 TBP-associated factor 13 protein [Capsic 0.968 0.961 0.809 2e-53
225437517128 PREDICTED: transcription initiation fact 0.992 1.0 0.798 6e-53
224128368129 predicted protein [Populus trichocarpa] 0.860 0.860 0.919 2e-52
332205181128 TBP-associated factor 13 [Solanum melong 0.976 0.984 0.795 2e-52
357442307136 Transcription initiation factor TFIID su 0.984 0.933 0.773 1e-51
>gi|255548497|ref|XP_002515305.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis] gi|223545785|gb|EEF47289.1| Transcription initiation factor TFIID subunit, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 119/129 (92%), Positives = 121/129 (93%), Gaps = 1/129 (0%)

Query: 1   MSNPSTGQSSKSKAGSSQPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDI 60
           MS+  TG SSKSK GSSQP ET SFKRKRGVFQKDLQHMMYGFGDDPNPLPE+VALVEDI
Sbjct: 1   MSSSFTGPSSKSKVGSSQPSET-SFKRKRGVFQKDLQHMMYGFGDDPNPLPESVALVEDI 59

Query: 61  VVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEV 120
           VVEYVTDLAHKAQDIGSK GKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEV
Sbjct: 60  VVEYVTDLAHKAQDIGSKRGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEV 119

Query: 121 DEEKLASVE 129
           DEEKLAS E
Sbjct: 120 DEEKLASAE 128

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|315937242|gb|ADU56179.1| transcription initiation factor TFIID subunit [Jatropha curcas] Back     alignment and taxonomy information
>gi|358248250|ref|NP_001240103.1| uncharacterized protein LOC100796504 [Glycine max] gi|255629011|gb|ACU14850.1| unknown [Glycine max] Back     alignment and taxonomy information
>gi|388515967|gb|AFK46045.1| unknown [Lotus japonicus] Back     alignment and taxonomy information
>gi|356534862|ref|XP_003535970.1| PREDICTED: transcription initiation factor TFIID subunit 13-like [Glycine max] Back     alignment and taxonomy information
>gi|390098822|gb|AFL48184.1| TBP-associated factor 13 protein [Capsicum annuum] Back     alignment and taxonomy information
>gi|225437517|ref|XP_002275358.1| PREDICTED: transcription initiation factor TFIID subunit 13-like isoform 3 [Vitis vinifera] gi|225437519|ref|XP_002275335.1| PREDICTED: transcription initiation factor TFIID subunit 13-like isoform 2 [Vitis vinifera] gi|225437521|ref|XP_002275286.1| PREDICTED: transcription initiation factor TFIID subunit 13-like isoform 1 [Vitis vinifera] gi|359480146|ref|XP_003632408.1| PREDICTED: transcription initiation factor TFIID subunit 13-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|224128368|ref|XP_002320312.1| predicted protein [Populus trichocarpa] gi|222861085|gb|EEE98627.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|332205181|gb|AEE36479.1| TBP-associated factor 13 [Solanum melongena] Back     alignment and taxonomy information
>gi|357442307|ref|XP_003591431.1| Transcription initiation factor TFIID subunit [Medicago truncatula] gi|217071536|gb|ACJ84128.1| unknown [Medicago truncatula] gi|355480479|gb|AES61682.1| Transcription initiation factor TFIID subunit [Medicago truncatula] gi|388501368|gb|AFK38750.1| unknown [Medicago truncatula] 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 ?
Query129
TAIR|locus:2196040126 TAF13 "TBP-associated factor 1 0.961 0.984 0.68 1.4e-39
UNIPROTKB|Q5ZLI0124 TAF13 "Uncharacterized protein 0.713 0.741 0.553 2.9e-23
UNIPROTKB|Q148M7124 TAF13 "Transcription initiatio 0.713 0.741 0.553 2.9e-23
UNIPROTKB|E2QZK3124 TAF13 "Uncharacterized protein 0.713 0.741 0.553 2.9e-23
UNIPROTKB|Q15543124 TAF13 "Transcription initiatio 0.713 0.741 0.553 2.9e-23
UNIPROTKB|F1S5Y9124 LOC100624071 "Uncharacterized 0.713 0.741 0.553 2.9e-23
MGI|MGI:1913500124 Taf13 "TAF13 RNA polymerase II 0.713 0.741 0.553 2.9e-23
RGD|1305398124 Taf13 "TAF13 RNA polymerase II 0.713 0.741 0.553 2.9e-23
FB|FBgn0032847136 Taf13 "TBP-associated factor 1 0.821 0.779 0.5 4.8e-23
ZFIN|ZDB-GENE-030131-2873124 taf13 "TAF13 RNA polymerase II 0.713 0.741 0.521 4.3e-22
TAIR|locus:2196040 TAF13 "TBP-associated factor 13" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 422 (153.6 bits), Expect = 1.4e-39, P = 1.4e-39
 Identities = 85/125 (68%), Positives = 96/125 (76%)

Query:     1 MSNPXXXXXXXXXXXXXXPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDI 60
             MSN                      KRK  +FQK+LQHMMYGFGD+ NPLPE+VALVEDI
Sbjct:     1 MSNTPAAAASSSSKSKAAGTSQPQEKRKT-LFQKELQHMMYGFGDEQNPLPESVALVEDI 59

Query:    61 VVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEV 120
             VVEYVTDL HKAQ+IGSK G+L V+DFLYLIRKDLPKLNRC ELL+MQEELKQARKAF+V
Sbjct:    60 VVEYVTDLTHKAQEIGSKRGRLLVDDFLYLIRKDLPKLNRCRELLAMQEELKQARKAFDV 119

Query:   121 DEEKL 125
             DE++L
Sbjct:   120 DEKEL 124
GO:0003677 "DNA binding" evidence=IEA
GO:0005634 "nucleus" evidence=ISM
GO:0005667 "transcription factor complex" evidence=ISS
GO:0006352 "DNA-dependent transcription, initiation" evidence=ISS
GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA;RCA
GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA
UNIPROTKB|Q5ZLI0 TAF13 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|Q148M7 TAF13 "Transcription initiation factor TFIID subunit 13" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2QZK3 TAF13 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q15543 TAF13 "Transcription initiation factor TFIID subunit 13" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1S5Y9 LOC100624071 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1913500 Taf13 "TAF13 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1305398 Taf13 "TAF13 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
FB|FBgn0032847 Taf13 "TBP-associated factor 13" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms
ZFIN|ZDB-GENE-030131-2873 taf13 "TAF13 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

ID ?Name ?Annotated EC number ?Identity ?Query coverage ?Hit coverage ?RBH(Q2H) ?RBH(H2Q) ?
Q148M7TAF13_BOVINNo assigned EC number0.55310.71310.7419yesno
Q15543TAF13_HUMANNo assigned EC number0.55310.71310.7419yesno
P61216TAF13_MOUSENo assigned EC number0.55310.71310.7419yesno
Q5R9W6TAF13_PONABNo assigned EC number0.55310.71310.7419yesno

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
eugene3.00140678
hypothetical protein (129 aa)
(Populus trichocarpa)
Predicted Functional Partners:
gw1.XVIII.2077.1
hypothetical protein (132 aa)
   •••• 0.825
estExt_fgenesh4_pm.C_LG_V0264
SubName- Full=Putative uncharacterized protein; (107 aa)
   • •• 0.687
estExt_Genewise1_v1.C_LG_I9297
SubName- Full=Putative uncharacterized protein; (175 aa)
    ••• 0.653
gw1.I.8107.1
hypothetical protein (222 aa)
    ••• 0.653
gw1.XIV.649.1
hypothetical protein (739 aa)
    ••• 0.622
eugene3.00061942
hypothetical protein (675 aa)
    ••• 0.585
estExt_fgenesh4_pm.C_LG_XVIII0164
hypothetical protein (676 aa)
    ••• 0.581
estExt_Genewise1_v1.C_LG_I4516
hypothetical protein (529 aa)
    ••• 0.565
estExt_Genewise1_v1.C_LG_IX3069
SubName- Full=Putative uncharacterized protein; (117 aa)
   • •  0.561
gw1.XIV.3608.1
hypothetical protein (532 aa)
    ••• 0.549

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 ?
Query129
cd0797892 cd07978, TAF13, The TATA Binding Protein (TBP) Ass 2e-42
pfam0226993 pfam02269, TFIID-18kDa, Transcription initiation f 2e-31
COG5248126 COG5248, TAF19, Transcription initiation factor TF 6e-24
>gnl|CDD|173962 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 
 Score =  134 bits (340), Expect = 2e-42
 Identities = 53/92 (57%), Positives = 72/92 (78%), Gaps = 1/92 (1%)

Query: 29  RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIG-SKGGKLSVEDF 87
           + +F K+++ MMYGFGD  NPLPETV L+EDIVVEY+ +L HKA ++   + GK+ VED 
Sbjct: 1   KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDL 60

Query: 88  LYLIRKDLPKLNRCTELLSMQEELKQARKAFE 119
           ++L+RKD  KL R  ELLSM++ELK+ARKAF+
Sbjct: 61  IFLLRKDPKKLARLRELLSMKDELKKARKAFD 92

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (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. 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. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the 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 are found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF13 interacts with TAF11 and makes a histone-like heterodimer similar to H3/H4-like proteins. The dimer may be structurally and functionally similar to the spt3 protein within the SAGA histone acetyltransferase complex. Length = 92
>gnl|CDD|190265 pfam02269, TFIID-18kDa, Transcription initiation factor IID, 18kD subunit Back     alignment and domain information
>gnl|CDD|227573 COG5248, TAF19, Transcription initiation factor TFIID, subunit TAF13 [Transcription] Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 129
cd0797892 TAF13 The TATA Binding Protein (TBP) Associated Fa 100.0
KOG3901109 consensus Transcription initiation factor IID subu 100.0
PF0226993 TFIID-18kDa: Transcription initiation factor IID, 100.0
COG5248126 TAF19 Transcription initiation factor TFIID, subun 99.97
KOG3902 352 consensus Histone acetyltransferase PCAF/SAGA, sub 99.92
cd0798172 TAF12 TATA Binding Protein (TBP) Associated Factor 97.37
PF0384768 TFIID_20kDa: Transcription initiation factor TFIID 97.28
smart0057677 BTP Bromodomain transcription factors and PHD doma 96.99
KOG1142258 consensus Transcription initiation factor TFIID, s 96.99
PF0080865 CBFD_NFYB_HMF: Histone-like transcription factor ( 96.81
PF0752477 Bromo_TP: Bromodomain associated; InterPro: IPR006 96.24
PLN00035103 histone H4; Provisional 96.05
PF1563076 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 95.97
smart0080365 TAF TATA box binding protein associated factor. TA 95.79
cd0007685 H4 Histone H4, one of the four histones, along wit 95.68
PTZ00015102 histone H4; Provisional 95.44
PF0012575 Histone: Core histone H2A/H2B/H3/H4 histone h2a si 95.37
cd07979117 TAF9 TATA Binding Protein (TBP) Associated Factor 94.96
COG203691 HHT1 Histones H3 and H4 [Chromatin structure and d 93.69
PF0296966 TAF: TATA box binding protein associated factor (T 92.67
smart0041774 H4 Histone H4. 91.59
KOG3902 352 consensus Histone acetyltransferase PCAF/SAGA, sub 90.62
PF02291129 TFIID-31kDa: Transcription initiation factor IID, 90.28
KOG0869168 consensus CCAAT-binding factor, subunit A (HAP3) [ 90.03
smart00428105 H3 Histone H3. 88.71
PLN00158116 histone H2B; Provisional 88.26
cd08050 343 TAF6 TATA Binding Protein (TBP) Associated Factor 83.29
PF05236 264 TAF4: Transcription initiation factor TFIID compon 82.25
>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 
Probab=100.00  E-value=3.9e-40  Score=232.69  Aligned_cols=91  Identities=58%  Similarity=1.005  Sum_probs=88.0

Q ss_pred             ccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh-cCCCCchhHHHHHHhhChhhHhHHHHHHHH
Q 033028           29 RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS-KGGKLSVEDFLYLIRKDLPKLNRCTELLSM  107 (129)
Q Consensus        29 k~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~-~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~~  107 (129)
                      ++.|.+||++|||||||+++|++|||.+|||||++||++||++|+++|. ++|++++|||+|+|||||+||+|+++||+|
T Consensus         1 ~~~f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~   80 (92)
T cd07978           1 KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDLIFLLRKDPKKLARLRELLSM   80 (92)
T ss_pred             CCccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999999999999999998 667899999999999999999999999999


Q ss_pred             HHHHHHHHhhcc
Q 033028          108 QEELKQARKAFE  119 (129)
Q Consensus       108 k~~ik~Ark~fd  119 (129)
                      +++||+|||+||
T Consensus        81 k~~~k~ark~~d   92 (92)
T cd07978          81 KDELKKARKAFD   92 (92)
T ss_pred             HHHHHHHHhccC
Confidence            999999999986

The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (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. 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. Several hy
>KOG3901 consensus Transcription initiation factor IID subunit [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
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription] Back     alignment and domain information
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription] 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
>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
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins 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
>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
>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
>PLN00035 histone H4; Provisional Back     alignment and domain information
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C Back     alignment and domain information
>smart00803 TAF TATA box binding protein associated factor 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
>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
>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
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics] 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
>smart00417 H4 Histone H4 Back     alignment and domain information
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription] 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
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription] Back     alignment and domain information
>smart00428 H3 Histone H3 Back     alignment and domain information
>PLN00158 histone H2B; Provisional 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
>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

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query129
1bh8_A45 Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Leng 2e-10
>pdb|1BH8|A Chain A, Htafii18HTAFII28 HETERODIMER CRYSTAL STRUCTURE Length = 45 Back     alignment and structure 
Iteration: 1

 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 36/45 (80%)
Query: 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDI 75
          +F K+L+ MMYGFGDD NP  E+V ++ED+V+E++T++ HKA  I
Sbjct: 1  LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSI 45

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query129
1bh9_A45 TAFII18; histone fold, tata binding protein, trans 3e-21
>1bh9_A TAFII18; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_A* Length = 45 Back     alignment and structure
 Score = 79.3 bits (196), Expect = 3e-21
 Identities = 24/45 (53%), Positives = 36/45 (80%)

Query: 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDI 75
          +F K+L+ MMYGFGDD NP  E+V ++ED+V+E++T++ HKA  I
Sbjct: 1  LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSI 45

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query129
1bh9_A45 TAFII18; histone fold, tata binding protein, trans 99.84
3b0b_B107 CENP-S, centromere protein S; histone fold, DNA bi 98.17
3b0c_T111 CENP-T, centromere protein T; histone fold, DNA bi 97.38
1id3_B102 Histone H4; nucleosome core particle, chromatin, p 96.88
2yfw_B103 Histone H4, H4; cell cycle, kinetochore, centromer 96.86
1tzy_D103 Histone H4-VI; histone-fold, tetramer-dimer-dimer, 96.85
1ku5_A70 HPHA, archaeal histon; histone fold, DNA binding p 96.85
3v9r_A90 MHF1, uncharacterized protein YOL086W-A; histone f 96.84
4dra_A113 Centromere protein S; DNA binding complex, DNA dam 96.82
2hue_C84 Histone H4; mini beta sheet, elongated beta sandwh 96.81
3vh5_A140 CENP-S; histone fold, chromosome segregation, DNA 96.75
1h3o_B76 Transcription initiation factor TFIID 20/15 kDa su 96.69
2byk_A140 Chrac-16; nucleosome sliding, histone fold, DNA-bi 96.63
1n1j_A93 NF-YB; histone-like PAIR, DNA binding protein; 1.6 96.61
1jfi_B179 DR1 protein, transcription regulator NC2 beta chai 96.59
2byk_B128 Chrac-14; nucleosome sliding, histone fold, DNA-bi 96.36
1b67_A68 Protein (histone HMFA); DNA binding protein; 1.48A 96.27
1n1j_B97 NF-YC; histone-like PAIR, DNA binding protein; 1.6 96.24
1taf_A68 TFIID TBP associated factor 42; transcription init 95.77
2ly8_A121 Budding yeast chaperone SCM3; centromere protein, 95.5
3b0c_W76 CENP-W, centromere protein W; histone fold, DNA bi 95.36
4g92_C119 HAPE; transcription factor, nucleosome, minor groo 94.92
1jfi_A98 Transcription regulator NC2 alpha chain; histone, 94.72
1f1e_A154 Histone fold protein; archaeal histone protein, DN 94.52
1taf_B70 TFIID TBP associated factor 62; transcription init 93.92
1f1e_A154 Histone fold protein; archaeal histone protein, DN 93.62
2l5a_A235 Histone H3-like centromeric protein CSE4, protein 92.68
3nqu_A140 Histone H3-like centromeric protein A; alpha helix 89.89
1tzy_B126 Histone H2B; histone-fold, tetramer-dimer-dimer, D 89.6
2hue_B77 Histone H3; mini beta sheet, elongated beta sandwh 89.57
4dra_E84 Centromere protein X; DNA binding complex, DNA dam 89.47
2nqb_D123 Histone H2B; nucleosome, NCP, chromatin, structura 89.04
2jss_A192 Chimera of histone H2B.1 and histone H2A.Z; histon 88.77
3vlf_B88 26S protease regulatory subunit 7 homolog; heat re 88.62
2f8n_G120 Core histone macro-H2A.1; nucleosome, NCP, macroh2 88.34
3r45_A156 Histone H3-like centromeric protein A; histone fol 87.47
1tzy_C136 Histone H3; histone-fold, tetramer-dimer-dimer, DN 86.91
3b0b_C81 CENP-X, centromere protein X; histone fold, DNA bi 86.82
2yfv_A100 Histone H3-like centromeric protein CSE4; cell cyc 86.6
3nqj_A82 Histone H3-like centromeric protein A; alpha helix 83.29
2nqb_C123 Histone H2A; nucleosome, NCP, chromatin, structura 81.36
1f66_C128 Histone H2A.Z; nucleosome, chromatin, histone vari 80.87
>1bh9_A TAFII18; histone fold, tata binding protein, transcription regulation complex; HET: PMB; 2.60A {Homo sapiens} SCOP: a.22.1.3 PDB: 1bh8_A* Back     alignment and structure
Probab=99.84  E-value=1.8e-21  Score=120.91  Aligned_cols=45  Identities=53%  Similarity=1.053  Sum_probs=43.3

Q ss_pred             ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033028           31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDI   75 (129)
Q Consensus        31 ~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~   75 (129)
                      +|++||++|||||||+++|++||+.+|||||++||+++|++|.++
T Consensus         1 lF~~ei~~mMy~fGD~~~P~~ETv~llEeiV~~~i~~l~~~A~~v   45 (45)
T 1bh9_A            1 LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSI   45 (45)
T ss_dssp             CCHHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            599999999999999999999999999999999999999999864
>3b0b_B CENP-S, centromere protein S; histone fold, DNA binding, DNA, nucleus, DNA binding protein; 2.15A {Gallus gallus} 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
>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
>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140} 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
>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2 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
>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
>3vh5_A CENP-S; histone fold, chromosome segregation, DNA binding, nucleus, binding protein; 2.40A {Gallus gallus} PDB: 3vh6_A 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
>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
>1n1j_A NF-YB; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 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
>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
>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
>1n1j_B NF-YC; histone-like PAIR, DNA binding protein; 1.67A {Homo sapiens} SCOP: a.22.1.3 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
>2ly8_A Budding yeast chaperone SCM3; centromere protein, CENH3 variants, partially unfolded; NMR {Saccharomyces cerevisiae} 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
>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
>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
>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
>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
>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
>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
>2hue_B Histone H3; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} 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
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_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
>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* 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
>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
>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
>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
>3nqj_A Histone H3-like centromeric protein A; alpha helix, histone fold, centromere, DNA binding protein; 2.10A {Homo sapiens} 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
>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

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 129
d1bh9a_45 a.22.1.3 (A:) TAF(II)18 {Human (Homo sapiens) [Tax 4e-21
>d1bh9a_ a.22.1.3 (A:) TAF(II)18 {Human (Homo sapiens) [TaxId: 9606]} Length = 45 Back     information, alignment and structure

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)18
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.7 bits (192), Expect = 4e-21
 Identities = 24/45 (53%), Positives = 36/45 (80%)

Query: 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDI 75
          +F K+L+ MMYGFGDD NP  E+V ++ED+V+E++T++ HKA  I
Sbjct: 1  LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSI 45

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query129
d1bh9a_45 TAF(II)18 {Human (Homo sapiens) [TaxId: 9606]} 99.86
d1htaa_68 Archaeal histone {Archaeon Methanothermus fervidus 97.25
d1ku5a_66 Archaeal histone {Archaeon (Pyrococcus horikoshii) 97.23
d1n1jb_78 Nuclear transcription factor Y subunit gamma (Nf-Y 96.87
d2huec182 Histone H4 {African clawed frog (Xenopus laevis) [ 96.82
d1h3ob_74 TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom 96.58
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 95.74
d1jfib_135 Negative cofactor 2, NC2, beta chain {Human (Homo 95.46
d1n1ja_87 Nuclear transcription factor Y subunit beta (Nf-Yb 95.44
d1tzyc_95 Histone H3 {Chicken (Gallus gallus), erythrocytes 95.12
d2bykb189 Chrac-14 {Fruit fly (Drosophila melanogaster) [Tax 95.02
d1jfia_66 Negative cofactor 2, NC2, alpha chain {Human (Homo 94.57
d1f1ea_151 Archaeal histone {Archaeon Methanopyrus kandleri [ 89.48
d1tafa_68 TAF(II)42 {Fruit fly (Drosophila melanogaster) [Ta 88.17
d1tafb_70 TAF(II)62 {Fruit fly (Drosophila melanogaster) [Ta 82.59
d2byka172 Chrac-16 {Fruit fly (Drosophila melanogaster) [Tax 82.58
>d1bh9a_ a.22.1.3 (A:) TAF(II)18 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=2.9e-22  Score=123.12  Aligned_cols=45  Identities=53%  Similarity=1.053  Sum_probs=43.4

Q ss_pred             ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033028           31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDI   75 (129)
Q Consensus        31 ~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~   75 (129)
                      +|++||++|||||||+++|++||+++|||||++||+++|++|+++
T Consensus         1 lF~~ei~~mMy~~GD~~~P~~ETv~llEdiv~~~i~~~~~~A~~v   45 (45)
T d1bh9a_           1 LFSKELRCMMYGFGDDQNPYTESVDILEDLVIEFITEMTHKAMSI   45 (45)
T ss_dssp             CCHHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            699999999999999999999999999999999999999999874
>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
>d1n1jb_ a.22.1.3 (B:) Nuclear transcription factor Y subunit gamma (Nf-Yc2) {Human (Homo sapiens) [TaxId: 9606]} 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
>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
>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
>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1tzyc_ a.22.1.1 (C:) Histone H3 {Chicken (Gallus gallus), erythrocytes [TaxId: 9031]} 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
>d1f1ea_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanopyrus kandleri [TaxId: 2320]} 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
>d1tafb_ a.22.1.3 (B:) TAF(II)62 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} 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