YRC Public Data Repository - Protein Structure Prediction

Protein:	NGR1_YEAST
Organism:	Saccharomyces cerevisiae S288c
Length:	672 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 NGR1_YEAST.

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 are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.462	a.4.1	Homeodomain-like
View	Download	0.435	a.60.1	SAM/Pointed domain
View	Download	0.462	a.60.2	RuvA domain 2-like
View	Download	0.524	a.60.3	C-terminal domain of RNA polymerase alpha subunit
View	Download	0.380	a.164.1	C-terminal domain of DFF45/ICAD (DFF-C domain)
View	Download	0.345	a.144.1	PABC (PABP) domain
View	Download	0.315	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.230	d.68.5	C-terminal domain of ProRS
View	Download	0.224	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.218	a.158.1	F-box 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 are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.397	a.74.1	Cyclin-like
View	Download	0.346	a.61.1	Retroviral matrix proteins
View	Download	0.364	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.425	a.5.4	Elongation factor TFIIS domain 2
View	Download	0.343	a.24.15	FAD-dependent thiol oxidase
View	Download	0.295	a.60.10	Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain
View	Download	0.277	d.110.1	Profilin (actin-binding protein)
View	Download	0.270	a.8.3	Families 57/38 glycoside transferase middle domain
View	Download	0.263	a.59.1	PAH2 domain
View	Download	0.263	a.25.2	Thermoplasma ferritin-like 4-helical bundle
View	Download	0.257	a.24.1	Apolipoprotein
View	Download	0.255	a.66.1	Transducin (alpha subunit), insertion domain
View	Download	0.236	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.224	a.26.1	4-helical cytokines
View	Download	0.219	a.19.1	Fertilization protein
View	Download	0.211	c.47.1	Thioredoxin-like
View	Download	0.205	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.203	f.18.1	F1F0 ATP synthase subunit A

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: