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PR00685

Identifier
TIFACTORIIB  [View Relations]  [View Alignment]  
Accession
PR00685
No. of Motifs
8
Creation Date
22-FEB-1997  (UPDATE 07-JUN-1999)
Title
Transcription initiation factor IIB signature
Database References

PROSITE; PS00782 TFIIB
PFAM; PF00382 transcript_fac2
INTERPRO; IPR000812
Literature References
1. HAWLEY, D.
Transcriptional activation - enter TFIIB
TRENDS BIOCHEM.SCI. 16 317-318 (1991).
 
2. HA, I., LANE, W.S. AND REINBERG, D.
Cloning of a human gene encoding the general transcription initiation
factor-IIB.
NATURE 352 689-695 (1991).

Documentation
In eukaryotes, transcription initiation by polymerase II is modulated by
both general and specific transcription factors. The general factors (which
include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through
common promoter elements, such as the TATA box. 
 
Transcription factor IIB (TFIIB) is of central importance in transcription
of class II genes: it associates with TFIID-TFIIA bound to DNA (the DA 
complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognized
by RNA polymerase II [1,2]. TFIIB comprises ~315-340 residues and contains
an imperfect C-terminal repeat of a 75-residue domain that may contribute
to the symmetry of the folded protein.
 
TIFACTORIIB is an 8-element fingerprint that provides a signature for
transcription initiation factor IIB. The fingerprint was derived from an
initial alignment of 9 sequences: the motifs were drawn from short conserved
regions spanning virtually the full alignment length, motif 4 including
part of the region encoded by PROSITE pattern TFIIB (PS00782), which lies
in the central section of the repeated domain. Two iterations on OWL29.1
were required to reach convergence, at which point a true set comprising 11
sequences was identified. Several partial matches were also found, all of
which are TFIIB transcription factor homologues or TFIIIB transcription
factors that fail to make a significant match with one or more motifs.
 
An update on SPTR37_9f identified a true set of 15 sequences, and 10
partial matches.
Summary Information
  15 codes involving  8 elements
1 codes involving 7 elements
0 codes involving 6 elements
1 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
5 codes involving 2 elements
Composite Feature Index
81515151515151515
701111111
600000000
500011111
400010111
321210000
250050000
12345678
True Positives
O13749        O26971        O28970        O59151        
TF2B_ARATH TF2B_DROME TF2B_HUMAN TF2B_KLULA
TF2B_METJA TF2B_PYRFU TF2B_RAT TF2B_SOYBN
TF2B_SULSH TF2B_XENLA TF2B_YEAST
True Positive Partials
Codes involving 7 elements
TF2B_PYRWO
Codes involving 5 elements
O58594
Codes involving 4 elements
O23215
Codes involving 3 elements
O16991 O82494
Codes involving 2 elements
Q13223 Q20429 Q92994 TF3B_CANAL
TF3B_KLULA
Sequence Titles
O13749      PROBABLE TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). 
O26971 TRANSCRIPTION INITIATION FACTOR TFIIB - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O28970 TRANSCRIPTION INITIATION FACTOR IIB - ARCHAEOGLOBUS FULGIDUS.
O59151 300AA LONG HYPOTHETICAL TRANSCRIPTION INITIATION FACTOR IIB - PYROCOCCUS HORIKOSHII.
TF2B_ARATH TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
TF2B_DROME TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - DROSOPHILA MELANOGASTER (FRUIT FLY).
TF2B_HUMAN TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - HOMO SAPIENS (HUMAN).
TF2B_KLULA TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - KLUYVEROMYCES LACTIS (YEAST).
TF2B_METJA TRANSCRIPTION INITIATION FACTOR IIB HOMOLOG (TFIIB) - METHANOCOCCUS JANNASCHII.
TF2B_PYRFU TRANSCRIPTION INITIATION FACTOR IIB HOMOLOG (TFIIB) - PYROCOCCUS FURIOSUS.
TF2B_RAT TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) (RNA POLYMERASE II ALPHA INITIATION FACTOR) - RATTUS NORVEGICUS (RAT).
TF2B_SOYBN TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - GLYCINE MAX (SOYBEAN).
TF2B_SULSH TRANSCRIPTION INITIATION FACTOR IIB HOMOLOG (TFIIB) - SULFOLOBUS SHIBATAE.
TF2B_XENLA TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
TF2B_YEAST TRANSCRIPTION INITIATION FACTOR IIB (TFIIB) (TRANSCRIPTION FACTOR E) - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).

TF2B_PYRWO TRANSCRIPTION INITIATION FACTOR IIB HOMOLOG (TFIIB) - PYROCOCCUS WOESEI.

O58594 208AA LONG HYPOTHETICAL TRANSCRIPTION INITIATION FACTOR IIB - PYROCOCCUS HORIKOSHII.

O23215 TRANSCRIPTION INITIATION FACTOR HOMOLOG - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).

O16991 W03F9.5 PROTEIN - CAENORHABDITIS ELEGANS.
O82494 T12H20.13 PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).

Q13223 TFIIIB 90 KDA SUBUNIT - HOMO SAPIENS (HUMAN).
Q20429 SIMILAR TO TRANSCRIPTION INITIATION FACTOR IIB - CAENORHABDITIS ELEGANS.
Q92994 TFIIB RELATED FACTOR HBRF - HOMO SAPIENS (HUMAN).
TF3B_CANAL TRANSCRIPTION FACTOR IIIB 70 KD SUBUNIT (TFIIIB) (B-RELATED FACTOR) (BRF) - CANDIDA ALBICANS (YEAST).
TF3B_KLULA TRANSCRIPTION FACTOR IIIB 70 KD SUBUNIT (TFIIIB) (B-RELATED FACTOR) (BRF1) - KLUYVEROMYCES LACTIS (YEAST).
Scan History
OWL29_1    2  100  NSINGLE    
SPTR37_9f 2 126 NSINGLE
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
YRAGDMICPECGLVVGDRVID TF2B_HUMAN 27 27 -
YRAGDMICPECGLVVGDRVID TF2B_RAT 27 27 -
YRAGDMICSECGLVVGDRVID TF2B_XENLA 27 27 -
YRAGDMICSECGLVVGDRVID TF2B_DROME 26 26 -
HSAGDTVCSECGLVLESHSID TF2B_SOYBN 19 19 -
HSAGDTLCSECGLVLESHSID TF2B_ARATH 19 19 -
FSEGDIVCALCGLVLSDRIVD TF2B_KLULA 42 42 -
AERGEYICSETGEVLEDKIID TF2B_SULSH 24 24 -
FSEGDVVCALCGLVLSDKLVD TF2B_YEAST 38 38 -

Motif 2 width=14
Element Seqn Id St Int Rpt
GSEWRTFSNDKATK TF2B_HUMAN 49 1 -
GSEWRTFSNDKATK TF2B_RAT 49 1 -
GSEWRTFSNDKAAA TF2B_XENLA 49 1 -
GSEWRTFSNEKSGV TF2B_DROME 48 1 -
TSEWRTFANESGDN TF2B_SOYBN 41 1 -
TSEWRTFANESSNS TF2B_ARATH 41 1 -
RSEWRTFSNDDQNG TF2B_KLULA 64 1 -
GPEWRAFTPEEKEK TF2B_SULSH 46 1 -
RSEWRTFSNDDHNG TF2B_YEAST 60 1 -

Motif 3 width=22
Element Seqn Id St Int Rpt
DPSRVGDSQNPLLSDGDLSTMI TF2B_HUMAN 63 0 -
DPSRVGDSQNPLLSDGDLSTMI TF2B_RAT 63 0 -
DPSRVGDAQNPLLSGGDLTTMI TF2B_XENLA 63 0 -
DPSRVGGPENPLLSGGDLSTII TF2B_DROME 62 0 -
DPNRVGGPSNPLLTDGGLSTVI TF2B_SOYBN 55 0 -
DPNRVGGPTNPLLADSALTTVI TF2B_ARATH 55 0 -
DPSRVGEASNPLLDGNHLTTRI TF2B_KLULA 79 1 -
KRSRVGGPLNNTIHDRGLSTLI TF2B_SULSH 59 -1 -
DPSRVGEASNPLLDGNNLSTRI TF2B_YEAST 75 1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
SACLYIACRQEGVPRTFKEI TF2B_HUMAN 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_RAT 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_XENLA 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_DROME 160 76 -
AACLYIACRQEDKPRTVKEI TF2B_SOYBN 153 76 -
AACLYIACRQEDKPRTIKEI TF2B_ARATH 152 75 -
ASVILVGCRRAEVGRSFKEI TF2B_KLULA 177 76 -
AAAIYAACRRMKLARTLDEI TF2B_SULSH 167 86 -
AASILIGCRRAEVARTFKEI TF2B_YEAST 173 76 -

Motif 5 width=16
Element Seqn Id St Int Rpt
SKKEIGRCFKLILKAL TF2B_HUMAN 187 6 -
SKKEIGRCFKLILKAL TF2B_RAT 187 6 -
SKKEIGRCFKLILKAL TF2B_XENLA 187 6 -
SKKEIGRCFKLTLKAL TF2B_DROME 186 6 -
TKKEIGRAKEYIVKQL TF2B_SOYBN 180 7 -
TKKEIGRAKDYIVKTL TF2B_ARATH 179 7 -
RKKEIGKTFTIIKNIL TF2B_KLULA 203 6 -
NRKEVARCYRLLLREL TF2B_SULSH 193 6 -
KTKEFGKTLNIMKNIL TF2B_YEAST 199 6 -

Motif 6 width=19
Element Seqn Id St Int Rpt
FMSRFCSNLCLPKQVQMAA TF2B_HUMAN 214 11 -
FMSRFCSNLCLPKQVQMAA TF2B_RAT 214 11 -
FMSRFCSNLGLTKQVQMAA TF2B_XENLA 214 11 -
FMCRFCANLDLPNMVQRAA TF2B_DROME 213 11 -
FMRRFCSNLCMNNQAVKAA TF2B_SOYBN 213 17 -
FMRRFCSNLAMSNHAVKAA TF2B_ARATH 212 17 -
FIPRFCSHLGLSVQVANAA TF2B_KLULA 244 25 -
YVTRIANLLGLSGRVMKTA TF2B_SULSH 220 11 -
YIPRFCSHLGLPMQVTTSA TF2B_YEAST 238 23 -

Motif 7 width=17
Element Seqn Id St Int Rpt
RSPISVAAAAIYMASQA TF2B_HUMAN 248 15 -
RSPISVAAAAIYMASQA TF2B_RAT 248 15 -
RSPISVAAAAIYMASQA TF2B_XENLA 248 15 -
RSPISVAAAAIYMASQA TF2B_DROME 247 15 -
RSPISIAAAVIYIITQL TF2B_SOYBN 245 13 -
RSPISIAAVVIYIITQL TF2B_ARATH 244 13 -
RSPITIAAAAIYMATLL TF2B_KLULA 278 15 -
KDPAGLAAAAIYIASLL TF2B_SULSH 254 15 -
KSPITIAVVSIYLNILL TF2B_YEAST 272 15 -

Motif 8 width=15
Element Seqn Id St Int Rpt
VADVTIRQSYRLIYP TF2B_HUMAN 280 15 -
VADVTIRQSYRLIYP TF2B_RAT 280 15 -
VADVTIRQSYRLIYP TF2B_XENLA 280 15 -
VADVTIRQSYKLMYP TF2B_DROME 279 15 -
VAEGTIRNSYKDLYP TF2B_SOYBN 277 15 -
VAEGTIRNSYKDLYP TF2B_ARATH 276 15 -
VTEGTVKGGYKALYE TF2B_KLULA 310 15 -
VTEVTVRNRYKELTQ TF2B_SULSH 286 15 -
VTEGTIKSGYKILYE TF2B_YEAST 304 15 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
YRAGDMICPECGLVVGDRVID TF2B_HUMAN 27 27 -
YRAGDMICPECGLVVGDRVID TF2B_RAT 27 27 -
YRAGDMICSECGLVVGDRVID TF2B_XENLA 27 27 -
YRAGDMICSECGLVVGDRVID TF2B_DROME 26 26 -
YRRGEFICQDCGLVIEDTYID O28970 42 42 -
YERAEIVCGKCGLVIDDNLVD O26971 26 26 -
HSAGDTVCSECGLVLESHSID TF2B_SOYBN 19 19 -
PERGEIVCARCGYVIEENIID O59151 19 19 -
PERGEIVCAKCGYVIEENIID TF2B_PYRFU 19 19 -
HSAGDTLCSECGLVLESHSID TF2B_ARATH 19 19 -
YERAEIVCAKCGCVIKEKLFD TF2B_METJA 54 54 -
FSSGDTVCGSCGLVLGDRIID O13749 34 34 -
FSEGDIVCALCGLVLSDRIVD TF2B_KLULA 42 42 -
AERGEYICSETGEVLEDKIID TF2B_SULSH 24 24 -
FSEGDVVCALCGLVLSDKLVD TF2B_YEAST 38 38 -

Motif 2 width=14
Element Seqn Id St Int Rpt
GSEWRTFSNDKATK TF2B_HUMAN 49 1 -
GSEWRTFSNDKATK TF2B_RAT 49 1 -
GSEWRTFSNDKAAA TF2B_XENLA 49 1 -
GSEWRTFSNEKSGV TF2B_DROME 48 1 -
GPEWRAFDSEQRDK O28970 64 1 -
GPEWRAFDHEQRDK O26971 48 1 -
TSEWRTFANESGDN TF2B_SOYBN 41 1 -
GPEWRAFDASQREK O59151 41 1 -
GPEWRAFDASQRER TF2B_PYRFU 41 1 -
TSEWRTFANESSNS TF2B_ARATH 41 1 -
GPEWRAFDHEQKIK TF2B_METJA 76 1 -
RSEWRTFSNSDEAS O13749 56 1 -
RSEWRTFSNDDQNG TF2B_KLULA 64 1 -
GPEWRAFTPEEKEK TF2B_SULSH 46 1 -
RSEWRTFSNDDHNG TF2B_YEAST 60 1 -

Motif 3 width=22
Element Seqn Id St Int Rpt
DPSRVGDSQNPLLSDGDLSTMI TF2B_HUMAN 63 0 -
DPSRVGDSQNPLLSDGDLSTMI TF2B_RAT 63 0 -
DPSRVGDAQNPLLSGGDLTTMI TF2B_XENLA 63 0 -
DPSRVGGPENPLLSGGDLSTII TF2B_DROME 62 0 -
KRSRVGAPVTYTIHDKGLSTII O28970 77 -1 -
KRTRVGAPITYTIHDKGLSTMI O26971 61 -1 -
DPNRVGGPSNPLLTDGGLSTVI TF2B_SOYBN 55 0 -
KRSRTGAPESILLHDKGLSTDI O59151 54 -1 -
RRSRTGAPESILLHDKGLSTEI TF2B_PYRFU 54 -1 -
DPNRVGGPTNPLLADSALTTVI TF2B_ARATH 55 0 -
VAGFGGFVLHNTIHDKGLSTVI TF2B_METJA 424 334 -
DPSRVGKVANPLLNGSQLDTTI O13749 71 1 -
DPSRVGEASNPLLDGNHLTTRI TF2B_KLULA 79 1 -
KRSRVGGPLNNTIHDRGLSTLI TF2B_SULSH 59 -1 -
DPSRVGEASNPLLDGNNLSTRI TF2B_YEAST 75 1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
SACLYIACRQEGVPRTFKEI TF2B_HUMAN 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_RAT 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_XENLA 161 76 -
SACLYIACRQEGVPRTFKEI TF2B_DROME 160 76 -
AAALYAACRQAGVPRTLDEI O28970 185 86 -
AASLYAACRKCNVPRTLDEI O26971 169 86 -
AACLYIACRQEDKPRTVKEI TF2B_SOYBN 153 76 -
AACVYAACRLLKVPRTLDEI O59151 156 80 -
AACVYAACRLLKVPRTLDEI TF2B_PYRFU 156 80 -
AACLYIACRQEDKPRTIKEI TF2B_ARATH 152 75 -
AAAIYAACRRCRVPRTLDEI TF2B_METJA 532 86 -
AACIYIACRQGKVPRTFMEI O13749 165 72 -
ASVILVGCRRAEVGRSFKEI TF2B_KLULA 177 76 -
AAAIYAACRRMKLARTLDEI TF2B_SULSH 167 86 -
AASILIGCRRAEVARTFKEI TF2B_YEAST 173 76 -

Motif 5 width=16
Element Seqn Id St Int Rpt
SKKEIGRCFKLILKAL TF2B_HUMAN 187 6 -
SKKEIGRCFKLILKAL TF2B_RAT 187 6 -
SKKEIGRCFKLILKAL TF2B_XENLA 187 6 -
SKKEIGRCFKLTLKAL TF2B_DROME 186 6 -
DRKEIGRTYRFITREL O28970 211 6 -
SKKEVGRTYRFLTREL O26971 195 6 -
TKKEIGRAKEYIVKQL TF2B_SOYBN 180 7 -
EKKEIGRSYRFIARNL O59151 182 6 -
DKKEIGRSYRFIARNL TF2B_PYRFU 182 6 -
TKKEIGRAKDYIVKTL TF2B_ARATH 179 7 -
DRKEIGRTYRFLAREL TF2B_METJA 558 6 -
PKKEIGRVYKTLQRML O13749 191 6 -
RKKEIGKTFTIIKNIL TF2B_KLULA 203 6 -
NRKEVARCYRLLLREL TF2B_SULSH 193 6 -
KTKEFGKTLNIMKNIL TF2B_YEAST 199 6 -

Motif 6 width=19
Element Seqn Id St Int Rpt
FMSRFCSNLCLPKQVQMAA TF2B_HUMAN 214 11 -
FMSRFCSNLCLPKQVQMAA TF2B_RAT 214 11 -
FMSRFCSNLGLTKQVQMAA TF2B_XENLA 214 11 -
FMCRFCANLDLPNMVQRAA TF2B_DROME 213 11 -
YIPRFCAALGLSGEVQKKA O28970 238 11 -
YVPRFASELGLSGEVQSKA O26971 222 11 -
FMRRFCSNLCMNNQAVKAA TF2B_SOYBN 213 17 -
YVNKFADELGLSEKVRRRA O59151 211 13 -
YVNKFADELGLSEKVRRRA TF2B_PYRFU 211 13 -
FMRRFCSNLAMSNHAVKAA TF2B_ARATH 212 17 -
YVPRFASELGLPGEVESKA TF2B_METJA 585 11 -
LMVRFCNRLMLPMSVQSAA O13749 235 28 -
FIPRFCSHLGLSVQVANAA TF2B_KLULA 244 25 -
YVTRIANLLGLSGRVMKTA TF2B_SULSH 220 11 -
YIPRFCSHLGLPMQVTTSA TF2B_YEAST 238 23 -

Motif 7 width=17
Element Seqn Id St Int Rpt
RSPISVAAAAIYMASQA TF2B_HUMAN 248 15 -
RSPISVAAAAIYMASQA TF2B_RAT 248 15 -
RSPISVAAAAIYMASQA TF2B_XENLA 248 15 -
RSPISVAAAAIYMASQA TF2B_DROME 247 15 -
RGPTGVAAAALYVASIL O28970 272 15 -
RGPTGVAAAALYIASVL O26971 256 15 -
RSPISIAAAVIYIITQL TF2B_SOYBN 245 13 -
KSPAGLVAAALYIASLL O59151 245 15 -
KSPAGLVAAALYIASLL TF2B_PYRFU 245 15 -
RSPISIAAVVIYIITQL TF2B_ARATH 244 13 -
RGPTGVAAAAIYIASVL TF2B_METJA 619 15 -
RSPISIAASGIYMISAL O13749 269 15 -
RSPITIAAAAIYMATLL TF2B_KLULA 278 15 -
KDPAGLAAAAIYIASLL TF2B_SULSH 254 15 -
KSPITIAVVSIYLNILL TF2B_YEAST 272 15 -

Motif 8 width=15
Element Seqn Id St Int Rpt
VADVTIRQSYRLIYP TF2B_HUMAN 280 15 -
VADVTIRQSYRLIYP TF2B_RAT 280 15 -
VADVTIRQSYRLIYP TF2B_XENLA 280 15 -
VADVTIRQSYKLMYP TF2B_DROME 279 15 -
VTEVTIRNRYKELAE O28970 304 15 -
VTEVTIRNRYKELTE O26971 288 15 -
VAEGTIRNSYKDLYP TF2B_SOYBN 277 15 -
VTEVTVRNRYKELVE O59151 277 15 -
VTEVTVRNRYKELVE TF2B_PYRFU 277 15 -
VAEGTIRNSYKDLYP TF2B_ARATH 276 15 -
VTEVTIRNRYKELTE TF2B_METJA 651 15 -
VSDSTIRIAYKLLHA O13749 301 15 -
VTEGTVKGGYKALYE TF2B_KLULA 310 15 -
VTEVTVRNRYKELTQ TF2B_SULSH 286 15 -
VTEGTIKSGYKILYE TF2B_YEAST 304 15 -