YRC Public Data Repository - Protein Structure Prediction

Protein:	NOP12
Organism:	Saccharomyces cerevisiae
Length:	459 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 NOP12.

Description	E-value	Query Range	Subject Range
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-88	[5..371]	[15..385]
PABP1_MOUSE - Polyadenylate-binding protein 1 OS=Mus musculus GN=Pabpc1 PE=1 SV=2	2.0E-88	[5..371]	[15..385]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	5.0E-88	[5..371]	[15..385]
gi\|2665654 - gi\|2665654\|gb\|AAB88449.1\| polyadenylate binding protein [Petromyzon marinus]	5.0E-87	[5..372]	[15..387]
gi\|19526272 - gi\|19526272\|gb\|AAL89666.1\|AF411956_7 polyA-binding protein [Takifugu rubripes]	1.0E-86	[5..372]	[15..386]
gi\|64970 - gi\|64970\|emb\|CAA40721.1\| polyA binding protein [Xenopus laevis]	3.0E-85	[5..380]	[15..394]

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Predicted Domain #1

Region A:
Residues: [1-90]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSAIDNLFG NIDEKKIESS VDKLFSSSCG PINKLEVKSK TRTVLPDSKK RERAAEADQE  60
   61 EKEASKPDVS DEQTEEVALP KVKKAKKSKR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.69897
Match:	1fj7A_
Description:	Nucleolin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.04120049976231	bayes_pls_golite062009
mRNA binding	4.29904003387927	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
	3.36965439092178	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.32565125258004	bayes_pls_golite062009
poly-pyrimidine tract binding	1.99190411806363	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
protein binding	0.89093640300829	bayes_pls_golite062009
snoRNA binding	0.87536768969411	bayes_pls_golite062009
snRNA binding	0.45487108214667	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [91-148]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NDEDEDLEAR YYAKLLNEEA EAEDDKPTVT KTDETSVPLT SAAKKVDFKE DELEKAER

[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	0.712	a.4.1	Homeodomain-like
View	Download	0.477	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.712	a.4.1	Homeodomain-like
View	Download	0.604	a.4.1	Homeodomain-like
View	Download	0.485	a.4.1	Homeodomain-like
View	Download	0.477	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.472	a.4.1	Homeodomain-like
View	Download	0.472	a.4.1	Homeodomain-like
View	Download	0.459	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.445	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.421	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.420	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.408	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.401	a.163.1	Crustacean CHH/MIH/GIH neurohormone
View	Download	0.389	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.385	a.65.1	Annexin
View	Download	0.362	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.343	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.340	a.153.1	Nuclear receptor coactivator interlocking domain
View	Download	0.334	a.4.10	N-terminal Zn binding domain of HIV integrase
View	Download	0.324	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.296	d.58.1	4Fe-4S ferredoxins
View	Download	0.288	g.1.1	Insulin-like
View	Download	0.240	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.235	d.50.3	PI-Pfui intein middle domain
View	Download	0.235	a.21.1	HMG-box
View	Download	0.226	a.140.1	LEM domain
View	Download	0.226	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.221	a.64.1	Saposin
View	Download	0.217	d.10.1	DNA-binding domain
View	Download	0.213	d.57.1	DNA damage-inducible protein DinI
View	Download	0.212	a.4.1	Homeodomain-like
View	Download	0.209	a.60.2	RuvA domain 2-like
View	Download	0.201	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.201	a.139.1	Type I dockerin domain

Predicted Domain #3

Region A:
Residues: [149-270]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TVFIGNILST VITSKKVYKE FKKLFGTNPI AETEESGNEK EEESSKKSDN NEFAIESIRF  60
   61 RSISFDEALP RKVAFVQQKF HKSRDTINAY IVYKNKSAVR KICSNLNAVV FQDHHLRVDS 120
  121 VA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	109.519517
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.04120049976231	bayes_pls_golite062009
mRNA binding	4.29904003387927	bayes_pls_golite062009
nucleic acid binding	3.81920018903278	bayes_pls_golite062009
	3.36965439092178	bayes_pls_golite062009
binding	3.05116833253954	bayes_pls_golite062009
single-stranded RNA binding	2.32565125258004	bayes_pls_golite062009
poly-pyrimidine tract binding	1.99190411806363	bayes_pls_golite062009
structural molecule activity	1.29928829870122	bayes_pls_golite062009
transcription regulator activity	1.07788694919471	bayes_pls_golite062009
DNA binding	0.978604858165557	bayes_pls_golite062009
protein binding	0.89093640300829	bayes_pls_golite062009
snoRNA binding	0.87536768969411	bayes_pls_golite062009
snRNA binding	0.45487108214667	bayes_pls_golite062009
transcription factor activity	0.234742017105535	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [271-372]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HPAPHDKKRS IFVGNLDFEE IEESLWKHFE PCGDIEYVRI IRDSKTNMGK GFAYVQFKDL  60
   61 QSVNKALLLN EKPMKSQKQE DENTKKPTKK ARKLRVSRCK NM

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	109.519517
Match:	1l3kA_
Description:	Nuclear ribonucleoprotein A1 (RNP A1, UP1)
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [373-459]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KKGTTIGTGL DRNGLTDSQR TRAGRAKKIL GKADRATLGQ EITIEGLRAK KGEGSTHLKK  60
   61 KKQRSATGRV TKRSIAFKKA QAEKSKK

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no 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: