YRC Public Data Repository - Protein Structure Prediction

Protein:	ABF2
Organism:	Saccharomyces cerevisiae
Length:	183 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 ABF2.

Description	E-value	Query Range	Subject Range
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	8.0E-36	[36..179]	[2..156]
HMGB3_CHICK - High mobility group protein B3 OS=Gallus gallus GN=HMGB3 PE=2 SV=2	9.0E-36	[36..179]	[2..156]
gi\|220953466, gi... - gi\|220953466\|gb\|ACL89276.1\| Dsp1-PA [synthetic construct], gi\|220943192\|gb\|ACL84139.1\| Dsp1-PA [synt... Dsp1-PA, Dsp1-PB... - The gene Dorsal switch protein 1 is referred to in FlyBase by the symbol Dmel\Dsp1 (CG12223, FBgn001...	6.0E-35	[4..180]	[132..327]
gi\|133892877\|ref... - (NM_008253) HMGB3 HMGB3_MOUSE - High mobility group protein B3 OS=Mus musculus GN=Hmgb3 PE=1 SV=3	7.0E-35	[36..179]	[2..156]
HMGB2_PIG - High mobility group protein B2 OS=Sus scrofa GN=HMGB2 PE=1 SV=2 gi\|108366 - pir\|\|A34719 nonhistone chromosomal protein HMG-2 - pig	3.0E-34	[37..179]	[3..158]
gi\|5764680 - gi\|5764680\|gb\|AAC27653.2\| high mobility group protein [Spalax ehrenbergi]	3.0E-34	[37..179]	[3..158]

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Predicted Domain #1

Region A:
Residues: [1-113]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNSYSLLTRS FHESSKPLFN LASTLLKASK RTQLRNELIK QGPKRPTSAY FLYLQDHRSQ  60
   61 FVKENPTLRP AEISKIAGEK WQNLEADIKE KYISERKKLY SEYQKAKKEF DEK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	68.36704
Match:	1hme__
Description:	HMG1, domains A and B
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	3.04393542109417	bayes_pls_golite062009
DNA binding	1.88326659692279	bayes_pls_golite062009
nucleic acid binding	1.85157640081091	bayes_pls_golite062009
chromatin binding	1.82810083714605	bayes_pls_golite062009
transcription regulator activity	1.34639198670075	bayes_pls_golite062009
protein binding	1.33904668423876	bayes_pls_golite062009
sequence-specific DNA binding	1.08208740778246	bayes_pls_golite062009
transcription factor activity	0.585772620695985	bayes_pls_golite062009
structure-specific DNA binding	0.45921402500371	bayes_pls_golite062009
transcription factor binding	0.19768703289845	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.16971196361447	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [114-183]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPPKKPAGPF IKYANEVRSQ VFAQHPDKSQ LDLMKIIGDK WQSLDQSIKD KYIQEYKKAI  60
   61 QEYNARYPLN

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.9
Match:	1j46A
Description:	SRY
Matching Structure (courtesy of the PDB):

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: