YRC Public Data Repository - Protein Structure Prediction

Protein:	NAB6
Organism:	Saccharomyces cerevisiae
Length:	1134 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 NAB6.

Description	E-value	Query Range	Subject Range
NAB6 - Putative RNA-binding protein that associates with mRNAs encoding cell wall proteins in high-throughp... NAB6_YEAST - RNA-binding protein NAB6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NAB6 PE=1 SV=1	0.0	[1..1134]	[1..1134]
PABP1_BOVIN - Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1 gi\|109087089 - gi\|109087089\|ref\|XP_001098239.1\| PREDICTED: poly(A) binding protein, cytoplasmic 1 isoform 2 [Macaca... gi\|123993665, gi... - gi\|168278070\|dbj\|BAG11013.1\| polyadenylate-binding protein 1 [synthetic construct], gi\|123999981\|gb\|... gi\|194036975 - gi\|194036975\|ref\|XP_001927782.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-bind... PABPC1 - poly(A) binding protein, cytoplasmic 1 gi\|73974130, gi\|... - gi\|73974178\|ref\|XP_857695.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-binding ...	2.0E-63	[584..947]	[20..382]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	3.0E-63	[584..947]	[20..382]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	3.0E-63	[584..947]	[20..382]
gi\|7673355 - gi\|7673355\|gb\|AAF66823.1\|AF190655_1 poly(A)-binding protein [Nicotiana tabacum]	7.0E-63	[567..843]	[110..393]
PABP8_ARATH - Polyadenylate-binding protein 8 OS=Arabidopsis thaliana GN=PAB8 PE=1 SV=1	8.0E-63	[567..843]	[128..411]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	8.0E-62	[584..947]	[20..383]

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Predicted Domain #1

Region A:
Residues: [1-118]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNSNSKKPV ANYAYRQQQD YNGMNAMVGN PMMYHPVDFV NGAGQYGPSQ HPAYYTNSPL  60
   61 PNIPPTPFDT AYGASLFPSH LLMGSPFVSS PNMQSGYNSA RSSNLKRKAY SRPVSNHN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [136-161]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VTPSNYYRMG RNSFSRNNNS TRNVTH

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [442-501]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VVSSARSSVA NIYEGKTSTH RLSVPSVTAG NNNDSNNNGN NNKSNMSGIT TLNNNSSIGV  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.82
Match:	1ruxA
Description:	Adenovirus hexon

Predicted Domain #2

Region A:
Residues: [119-135]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GYNGNSNSNQ NNTNNGM

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [162-287]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNNKGCDTRN NSGRRTFARN NIFDDILPEM LLQRPFCINY KVLPTGDDAY RTRSLLIENV  60
   61 DHSIDLHSIV KNFVKSNTLE SAYLIEGGKS DDSKDVETKN LSILISFLTK GDCLNFYNNI 120
  121 LQRLSE

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [325-350]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EEADITNGST MISASLHHNI ANKDAT

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.82
Match:	1ruxA
Description:	Adenovirus hexon

Predicted functions:

Term	Confidence	Notes
binding	1.46194714498106	bayes_pls_golite062009
nucleic acid binding	0.889591023319018	bayes_pls_golite062009
RNA binding	0.535898980134848	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [288-324]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FKTFLKSEAL NLKFVCLNYD PKCLPTFIES EALTENA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [351-441]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RSIIIEFKSP VEKSDLFKKK LQFLDRSKNK RYILESIDLV NTDVPSNQFP ENYAVLTFLN  60
   61 ISMAIEVLDY LKKYSKNLGI SKCFYVSLAP L

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [502-552]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SVYGHSNMSL TSLSSSVSLN EEIDMLATKL QGVELDGTYL EINYRDYQTP T

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.82
Match:	1ruxA
Description:	Adenovirus hexon

Predicted Domain #4

Region A:
Residues: [553-636]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IEEHSTHLSN VKISKTTENS RQFSQDIPSP LPLNEHMFMN DSNQSNGAII PQQLIATPSP  60
   61 VSPNLQMNQR VLPNPITQSL EQNF

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.97
Match:	1k28D
Description:	Baseplate structural protein gp27
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [637-726]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NVSAKVASSM GSDIGNRTIY IGNINPRSKA EDICNVVRGG ILQSIKYIPE KKICFVTFIE  60
   61 APSAVQFYAN SFIDPIVLHG NMLRVGWGHY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.0
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [727-846]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGPLPKLISL AVTIGASRNV YVSLPEFAFK EKFIHDPQYK KLHETLSLPD AEQLREDFST  60
   61 YGDIEQINYL SDSHCCWINF MNISSAISLV EEMNKESTVQ NESGEVTLKR ATEEKFGGRY 120
  121

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.0
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [847-909]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KGLLINYGKD RCGNINKNLI AGKNSRFYKK VKRPSYNIRL SKLEEKRRQN EIDEKEKAFD  60
   61 KPL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #8

Region A:
Residues: [910-1077]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NLESLGISLD AHKDNGGGET GTANNTGHEN ESELEAENEN GNETGSFGGL GLAVASSDVK  60
   61 RATSDETDYE DIFNKSSGSS DSSSDVEVIM HSPSDPEYAL KSQTLRSSSQ TVINSKRPVK 120
  121 IEDEEEAVGM SQLNYRSSLR QAPPRAPSTL SYNHSKNNET PMQDIFTN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #9

Region A:
Residues: [1078-1134]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GETANNRKKK RGSFARHRTI PGSDVMAQYL AQVQHSTFMY AANILGASAE DNTHPDE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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: