YRC Public Data Repository - Protein Structure Prediction

Protein:	NGR1
Organism:	Saccharomyces cerevisiae
Length:	672 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 NGR1.

Description	E-value	Query Range	Subject Range
NGR1 - RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochon... NGR1_YEAST - Negative growth regulatory protein NGR1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..672]	[1..672]
gi\|12855391, gi\|... - gi\|26325704\|dbj\|BAC26606.1\| unnamed protein product [Mus musculus], gi\|255652857\|ref\|NP_001157308.1\|...	0.0	[25..645]	[2..567]
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 ...	7.0E-95	[183..645]	[2..560]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	2.0E-93	[183..645]	[2..560]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	6.0E-93	[33..648]	[1..565]
pAbp-PB, pAbp-PA... - The gene polyA-binding protein is referred to in FlyBase by the symbol Dmel\pAbp (CG5119, FBgn000303... gi\|195335482, gi... - gi\|195335482\|ref\|XP_002034394.1\| GM21847 [Drosophila sechellia], gi\|194126364\|gb\|EDW48407.1\| GM21847... gi\|220946756 - gi\|220946756\|gb\|ACL85921.1\| pAbp-PA [synthetic construct]	1.0E-91	[33..641]	[1..567]

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Predicted Domain #1

Region A:
Residues: [1-86]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MMSNVANASQ RQENPYIIPL PPSSTVETST EPPRTLWMGD LDPSFDEATI EEIWSKLDKK  60
   61 VIVKLIRAKK NLLIPCSSTS SSNNNT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	92.54902
Match:	1cvjA_
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	3.27266833016156	bayes_pls_golite062009
binding	2.80563734517858	bayes_pls_golite062009
nucleic acid binding	2.18035791990719	bayes_pls_golite062009
mRNA binding	2.17710836425586	bayes_pls_golite062009
protein binding	1.02232785292059	bayes_pls_golite062009
	0.787367154319901	bayes_pls_golite062009
single-stranded RNA binding	0.419268956417989	bayes_pls_golite062009
structural molecule activity	0.106871867442361	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [87-184]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SEENAENQQS ASNSTDQLDN SQMININGIS FIDPSTTQLH HAGYCFVEFE TQKDAKFALS  60
   61 LNATPLPNFY SPTTNSQTNP TFKRTFRLNW ASGATLQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	89.28043
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	3.27266833016156	bayes_pls_golite062009
binding	2.80563734517858	bayes_pls_golite062009
nucleic acid binding	2.18035791990719	bayes_pls_golite062009
mRNA binding	2.17710836425586	bayes_pls_golite062009
protein binding	1.02232785292059	bayes_pls_golite062009
	0.787367154319901	bayes_pls_golite062009
single-stranded RNA binding	0.419268956417989	bayes_pls_golite062009
structural molecule activity	0.106871867442361	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [185-306]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SIPSTPEFSL FVGDLSPTAT EADLLSLFQT RFKSVKTVRV MTDPLTGSSR CFGFVRFGDE  60
   61 DERRRALIEM SGKWFQGRAL RVAYATPRNN MMLQLQEQQQ QQQQLQQQHQ QLDQEDNNGP 120
  121 LL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	89.28043
Match:	1fxlA_
Description:	Hu antigen D (Hud)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	3.27266833016156	bayes_pls_golite062009
binding	2.80563734517858	bayes_pls_golite062009
nucleic acid binding	2.18035791990719	bayes_pls_golite062009
mRNA binding	2.17710836425586	bayes_pls_golite062009
protein binding	1.02232785292059	bayes_pls_golite062009
	0.787367154319901	bayes_pls_golite062009
single-stranded RNA binding	0.419268956417989	bayes_pls_golite062009
structural molecule activity	0.106871867442361	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [307-358]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IKTANNLIQN NSNMLPLNAL HNAPPMHLNE GGISNMRVND SLPSNTYNTD PT

[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 #5

Region A:
Residues: [359-475]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NTTVFVGGLV PKTTEFQLRS LFKPFGPILN VRIPNGKNCG FVKFEKRIDA EASIQGLQGF  60
   61 IVGGSPIRLS WGRPSSSNAK TNSTIMGASQ YMSSNGLRAP SAASSVDNSK QILEQYA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.221849
Match:	1h6kX_
Description:	CBP20, 20KDa nuclear cap-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [476-584]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDKRRLFLHQ QQQQQQQQQQ DGNFSMEQMA HNNYYNYNNY DYHRNKNGSH SDLVNLQRSN  60
   61 VPYMQEDGAL YPHQYSSPSY SLHPTGNQFS NATNNLPQFG NAMSISMQL

[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 #7

Region A:
Residues: [585-672]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PNGNSNKTAS SMNTNPNTNM IMNSNMNMNM NVNPVPYGMG NGANMYDVSR MMTPPLNIAP  60
   61 NSNNSKSSIM NKHPNRNNVP PIHPSLLH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11.0
Match:	1g9lA_
Description:	poly(A) binding protein
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:

Predicted functions:

Predicted functions: