YRC Public Data Repository - Protein Structure Prediction

Protein:	T2FB_MOUSE
Organism:	Mus musculus
Length:	249 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for T2FB_MOUSE.

Description	E-value	Query Range	Subject Range
gi\|73989304 - gi\|73989304\|ref\|XP_851466.1\| PREDICTED: similar to general transcription factor IIF, polypeptide 2 [...	394.0	[0..1]	[249..108]
T2FB_BOVIN - General transcription factor IIF subunit 2 OS=Bos taurus GN=GTF2F2 PE=2 SV=1	382.0	[0..1]	[249..1]
HGNC:4653\|MIM:18... - transcription factor IIF, polypeptide 2, 30kDa gi\|114651459 - gi\|114651459\|ref\|XP_001154142.1\| PREDICTED: general transcription factor IIF, polypeptide 2, 30kDa [... gi\|61356697, gi\|... - gi\|61356697\|gb\|AAX41274.1\| general transcription factor IIF polypeptide 2 [synthetic construct], gi\|... GTF2F2 - general transcription factor IIF, polypeptide 2, 30kDa	381.0	[0..1]	[249..1]
gi\|31542922, gi\|... - gi\|60552080\|gb\|AAH91112.1\| General transcription factor IIF, polypeptide 2 [Rattus norvegicus], pir\|...	381.0	[0..1]	[249..1]
CCDS9395.1_1 - null gi\|109120627 - gi\|109120627\|ref\|XP_001094507.1\| PREDICTED: general transcription factor IIF, polypeptide 2, 30kDa [...	380.0	[0..1]	[249..1]
gi\|62901918 - gi\|62901918\|gb\|AAY18910.1\| RAP30 [synthetic construct]	380.0	[0..2]	[249..26]
gi\|50730835 - gi\|50730835\|ref\|XP_417039.1\| PREDICTED: similar to General transcription factor IIF, polypeptide 2 [...	374.0	[0..1]	[249..79]
gi\|38174399, gi\|... - gi\|45360629\|ref\|NP_988987.1\| general transcription factor 2F, polypeptide 2, 30kDa [Xenopus (Siluran...	358.0	[0..2]	[249..3]

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Predicted Domain #1

Region A:
Residues: [1-119]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAERGELDLT GAKQNTGVWL VKVPKYLSQQ WAKASGRGEV GKLRIAKNQG RTEVSFTLNE  60
   61 DLANIHDIGG KPASVSAPRE HPFVLQSVGG QTLTVFTESS SDKLSLEGIV VQRAECRPA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	47.39794
Match:	1f3uA
Description:	TFIIF beta subunit, Rap30
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	10.2797850053222	bayes_pls_golite062009
transcription initiation factor activity	6.22439849848084	bayes_pls_golite062009
RNA polymerase II transcription factor activity	4.06672086326535	bayes_pls_golite062009
transcription regulator activity	3.89911747857156	bayes_pls_golite062009
binding	2.17316238057078	bayes_pls_golite062009
transcription activator activity	2.12958061949296	bayes_pls_golite062009
protein binding	1.90482509358938	bayes_pls_golite062009
transcription coactivator activity	1.30173573105398	bayes_pls_golite062009
transcription factor binding	0.677361513203971	bayes_pls_golite062009
transcription cofactor activity	0.43974291826617	bayes_pls_golite062009
catalytic activity	0.304516551414824	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [120-249]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ASENYMKLKR LQIEESSKPV RLSQQLDKVV TTNYKPVANH QYNIEYERKK KEDGKRARAD  60
   61 KQHVLDMLFS AFEKHQYYNL KDLVDITKQP VGYLKEILKE IGIQNVKGIH KNTWELKPEY 120
  121 RHYQTEEKSD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.30103
Match:	1bbyA
Description:	DNA-BINDING DOMAIN FROM HUMAN RAP30, NMR, MINIMIZED AVERAGE
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	5.67074370996647	bayes_pls_golite062009
transcription regulator activity	5.55329976718261	bayes_pls_golite062009
DNA binding	5.08959163553491	bayes_pls_golite062009
nucleic acid binding	4.99681957904233	bayes_pls_golite062009
transcription factor activity	4.33152142980289	bayes_pls_golite062009
transcription activator activity	3.70589483230587	bayes_pls_golite062009
sequence-specific DNA binding	3.58179858678904	bayes_pls_golite062009
binding	3.52874320222492	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.60738445921725	bayes_pls_golite062009
transcription repressor activity	2.22485867684613	bayes_pls_golite062009
DNA-directed RNA polymerase activity	1.82365519759474	bayes_pls_golite062009
RNA polymerase activity	1.82365519759474	bayes_pls_golite062009
transcription elongation regulator activity	1.81270943531115	bayes_pls_golite062009
protein binding	1.80415286835431	bayes_pls_golite062009
RNA binding	0.992043085614693	bayes_pls_golite062009
transcription factor binding	0.85714789329232	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	0.66743181561551	bayes_pls_golite062009
nucleotidyltransferase activity	0.237727660028553	bayes_pls_golite062009
RNA polymerase II transcription factor activity, enhancer binding	0.23177057841536	bayes_pls_golite062009
positive transcription elongation factor activity	0.13524243942225	bayes_pls_golite062009
structural molecule activity	0.111941063082739	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: