YRC Public Data Repository - Protein Structure Prediction

Protein:	RIM4_YEAST
Organism:	Saccharomyces cerevisiae S288c
Length:	713 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 RIM4_YEAST.

Description	E-value	Query Range	Subject Range
RIM4 - Putative RNA-binding protein required for the expression of early and middle sporulation genes RIM4_YEAST - Meiotic activator RIM4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RIM4 PE=1 SV=1	0.0	[1..713]	[1..713]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	0.0	[84..557]	[2..493]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	0.0	[84..558]	[2..494]
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 ...	0.0	[84..558]	[2..494]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	0.0	[84..571]	[2..518]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	0.0	[84..562]	[2..509]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	0.0	[84..555]	[2..490]
gi\|7673355 - gi\|7673355\|gb\|AAF66823.1\|AF190655_1 poly(A)-binding protein [Nicotiana tabacum]	0.0	[71..580]	[5..573]

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Predicted Domain #1

Region A:
Residues: [1-73]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKTEISTADS LRDPPSNGLK ADSELVIRED IDQFLPSEVS SLGSDHQNDG EDSDTDSDNF  60
   61 LQDPEDDVDE EST

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.916	N/A	N/A	a.23.5	Hemolysin expression modulating protein HHA

Predicted Domain #2

Region A:
Residues: [74-229]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GRGTVTTTST STESRGRPSS CIFVASLAAA LSDDELCLSV TENFKKYGDL ARVKVLRDNA  60
   61 NRPYAFVQYN NDHDAKHALI RAQGTLLNGR RLRCEPAKVN RTLYLKNQQS IDFNEISQIC 120
  121 EKFGGLEQIV PDRTDNQYTR RYTYPISSAN SWFVQF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	45.154902
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	3.03004688154589	bayes_pls_golite062009
binding	2.41127885655304	bayes_pls_golite062009
RNA binding	1.96321378335448	bayes_pls_golite062009
protein binding	1.14508556628804	bayes_pls_golite062009
mRNA binding	0.79383576791259	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [230-331]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VYRDDAIRAY ANLRTDPNWI IEWAQNINVP KNYNLLHKSK FKSSKYHQNN GIINNDGSNN  60
   61 NDNNNSNNNN REDSRRNGDV IEEECGHVHG SDSEEKLTSD GI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.154902
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	3.03004688154589	bayes_pls_golite062009
binding	2.41127885655304	bayes_pls_golite062009
RNA binding	1.96321378335448	bayes_pls_golite062009
protein binding	1.14508556628804	bayes_pls_golite062009
mRNA binding	0.79383576791259	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [332-428]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YDDEDKDSEI TIDKRSIFVG QLDKETTREE LNRRFSTHGK IQDINLIFKP TNIFAFIKYE  60
   61 TEEAAAAALE SENHAIFLNK TMHVQYKEVG GRHNRKF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.154902
Match:	2up1A_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [429-574]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGKNGGSNFN HHQFFSTRSG KTFTGPELNL APPPINMYRK MSGGSQQESE TMMPYMPMGP  60
   61 MPMGPPPPNA ASLSDFDMFP PSYSTFMKGM MPLRRKSMPN SWSSPSSKSV NSENESVNGG 120
  121 DENSELPSEI PESSGRYNAA NSFTTY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	3.30103
Match:	1deqA_
Description:	Fibrinogen
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [575-713]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNSSAGNSNN NNNNNNSNSN KSQYKKRYAR RSSYGYNEVP PKPYYFQPYY YHPMQYHMGP  60
   61 MGPLHPSQGS AGNHHPYMMV YPMSPPPPSG LDGSMIPPPI NVSQSHAANH GSTHVHANEF 120
  121 ISNDTGDINE DNKAYSLDY

[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.

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: