YRC Public Data Repository - Protein Structure Prediction

Protein:	HEK2
Organism:	Saccharomyces cerevisiae
Length:	381 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 HEK2.

Description	E-value	Query Range	Subject Range
HEK2 - RNA binding protein involved in the asymmetric localization of ASH1 mRNA; represses translation of A... HEK2_YEAS7 - Heterogeneous nuclear rnp K-like protein 2 OS=Saccharomyces cerevisiae (strain YJM789) GN=HEK2 PE=3 ... HEK2_YEAST - Heterogeneous nuclear rnp K-like protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ...	9.0E-63	[1..381]	[1..381]
IF2B3_DANRE - Insulin-like growth factor 2 mRNA-binding protein 3 OS=Danio rerio GN=igf2bp3 PE=1 SV=1	2.0E-54	[3..353]	[233..580]
gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase [Escherichia coli O157:H7], gi\|13363518\|db... gi\|74313701, gi\|... - gi\|74313701\|ref\|YP_312120.1\| polynucleotide phosphorylase/polyadenylase [Shigella sonnei Ss046], gi\|... gi\|209920641, gi... - gi\|209920641\|ref\|YP_002294725.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli SE11],... gi\|209758380, gi... - pir\|\|H85979 polynucleotide phosphorylase [imported] - Escherichia coli (strain O157:H7, substrain E... gi\|218353603, gi... - gi\|218696871\|ref\|YP_002404538.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli 55989]... gi\|218701935, gi... - gi\|218701935\|ref\|YP_002409564.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli IAI39]... gi\|12517775, gi\|... - gi\|15803706\|ref\|NP_289740.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 ED... gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 st...	7.0E-52	[23..369]	[329..687]
PNP_YERPP - Polyribonucleotide nucleotidyltransferase OS=Yersinia pestis (strain Pestoides F) GN=pnp PE=3 SV=1 gi\|166010063, gi... - gi\|166010063\|ref\|ZP_02230961.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis biovar An... gi\|165922487, gi... - gi\|165925875\|ref\|ZP_02221707.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis biovar Or... gi\|167420765, gi... - gi\|167420765\|ref\|ZP_02312518.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis biovar Or... gi\|166204545, gi... - gi\|166214313\|ref\|ZP_02240348.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis biovar An... gi\|229695508, gi... - gi\|229839142\|ref\|ZP_04459301.1\| polynucleotide phosphorylase/polyadenylase [Yersinia pestis biovar O... PNP_YERPY - Polyribonucleotide nucleotidyltransferase OS=Yersinia pseudotuberculosis serotype O:3 (strain YPIII)... gi\|229896631, gi... - gi\|229896631\|ref\|ZP_04511798.1\| polynucleotide phosphorylase/polyadenylase [Yersinia pestis Pestoide... gi\|167423666, gi... - gi\|167423666\|ref\|ZP_02315419.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis biovar Me... gi\|229687198, gi... - gi\|229899706\|ref\|ZP_04514847.1\| polynucleotide phosphorylase/polyadenylase [Yersinia pestis biovar O... gi\|165936694, gi... - gi\|89105035\|ref\|ZP_01177562.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_YERPA - Polyribonucleotide nucleotidyltransferase OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=pnp PE=... gi\|149289107, gi... - gi\|153997470\|ref\|ZP_02022570.1\| polyribonucleotide nucleotidyltransferase [Yersinia pestis CA88-4125... PNP_YERPE - Polyribonucleotide nucleotidyltransferase OS=Yersinia pestis GN=pnp PE=3 SV=1 PNP_YERPG - Polyribonucleotide nucleotidyltransferase OS=Yersinia pestis bv. Antiqua (strain Angola) GN=pnp PE=3... PNP_YERP3 - Polyribonucleotide nucleotidyltransferase OS=Yersinia pseudotuberculosis serotype O:1b (strain IP 31... gi\|218930504, gi... - gi\|218930504\|ref\|YP_002348379.1\| polynucleotide phosphorylase/polyadenylase [Yersinia pestis CO92], ...	7.0E-52	[23..369]	[306..664]
IF23B_XENLA - Insulin-like growth factor 2 mRNA-binding protein 3-B OS=Xenopus laevis GN=igf2bp3-b PE=1 SV=1	7.0E-52	[3..331]	[243..570]
EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... gi\|194422295, gi... - gi\|83585805\|ref\|ZP_00924446.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_ECOBW - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=pnp ... PNP_ECOHS - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O9:H4 (strain HS) GN=pnp PE=3 SV=1 gi\|253323044, gi... - gi\|253772000\|ref\|YP_003034831.1\| Polyribonucleotide nucleotidyltransferase [Escherichia coli BL21(DE... gi\|254038330, gi... - gi\|254038330\|ref\|ZP_04872388.1\| polynucleotide phosphorylase/polyadenylase [Escherichia sp. 1_1_43],... PNP_ECOLI - Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (Polynucleotide phosphorylase) (PNPase) - Esc... PNP_ECODH - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / DH10B) GN=pnp PE=3 SV=2	1.0E-51	[23..369]	[306..664]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	4.0E-51	[23..369]	[329..687]
PNP_SALCH - Polyribonucleotide nucleotidyltransferase OS=Salmonella choleraesuis GN=pnp PE=3 SV=2 PNP_SALPA - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi A (strain ATCC 9150 / SARB42) GN=p... PNP_SALG2 - Polyribonucleotide nucleotidyltransferase OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=p... PNP_SALEP - Polyribonucleotide nucleotidyltransferase OS=Salmonella enteritidis PT4 (strain P125109) GN=pnp PE=3... PNP_SALPK - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi A (strain AKU_12601) GN=pnp PE=3 S... PNP_SALTY - Polyribonucleotide nucleotidyltransferase OS=Salmonella typhimurium GN=pnp PE=1 SV=1 PNP_SALPB - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN... PNP_SALPA - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi A GN=pnp PE=3 SV=1 PNP_SALPB - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN... PNP_SALCH - Polyribonucleotide nucleotidyltransferase OS=Salmonella choleraesuis (strain SC-B67) GN=pnp PE=3 SV=... PNP_SALPC - Polyribonucleotide nucleotidyltransferase OS=Salmonella paratyphi C (strain RKS4594) GN=pnp PE=3 SV=... PNP_SALTY - Polyribonucleotide nucleotidyltransferase OS=Salmonella typhimurium GN=pnp PE=1 SV=1 PNP_SALCH - Polyribonucleotide nucleotidyltransferase OS=Salmonella choleraesuis GN=pnp PE=3 SV=2 lcl\|NC_016856.1_... - [gene=pnp] [protein=polynucleotide phosphorylase/polyadenylase] [protein_id=YP_005239459.1] [locatio... PNP_SALTY - Polyribonucleotide nucleotidyltransferase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 70...	5.0E-51	[23..369]	[306..664]

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Predicted Domain #1

Region A:
Residues: [1-42]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSQFFEAATP VAIPTNNTNG GSSDAGSAAT GGAPVVGTTA QP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [165-238]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSHISSIIGK AGATIKSLIN KHGVKIVASK DFLPASDERI IEIQGFPGSI TNVLIEISEI  60
   61 ILSDVDVRFS TERS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.9432182987214	bayes_pls_golite062009
structural constituent of ribosome	3.63349555627235	bayes_pls_golite062009
structural molecule activity	3.43604616110432	bayes_pls_golite062009
nucleic acid binding	2.14875774646095	bayes_pls_golite062009
binding	1.9759530321894	bayes_pls_golite062009
nucleotidyltransferase activity	1.69410216708845	bayes_pls_golite062009
DNA binding	1.688021219058	bayes_pls_golite062009
deacetylase activity	1.09789613642093	bayes_pls_golite062009
exonuclease activity	1.02947145936572	bayes_pls_golite062009
transcription termination factor activity	1.01912880224809	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.96549462572212	bayes_pls_golite062009
ribonuclease activity	0.75307991342421	bayes_pls_golite062009
protein binding	0.523813050066193	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.499351238958464	bayes_pls_golite062009
3'-5'-exoribonuclease activity	0.48105441429954	bayes_pls_golite062009
3'-5' exonuclease activity	0.477960254167	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.36703663415044	bayes_pls_golite062009
exoribonuclease activity	0.350394896843651	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.337324481645901	bayes_pls_golite062009
DNA-(apurinic or apyrimidinic site) lyase activity	0.288026663667102	bayes_pls_golite062009
RNA binding	0.24714225183821	bayes_pls_golite062009
kinase activity	0.237670019875888	bayes_pls_golite062009
damaged DNA binding	0.16864489654021	bayes_pls_golite062009
catalytic activity	0.10089766806364	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.0869020377778909	bayes_pls_golite062009
pyrophosphatase activity	0.0193674670513169	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [43-164]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TINHRLLLSL KEAAKIIGTK GSTISRIRAA NAVKIGISEK VPGCSDRILS CAGNVINVAN  60
   61 AIGDIVDVLN KRNPENEDAA EGEAEEHYYF HFLNHILPAP SKDEIRDLQQ LEDIGYVRLI 120
  121 VA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [239-381]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YFPHLKKSSG EPTSPSTSSN TRIELKIPEL YVGAIIGRGM NRIKNLKTFT KTNIVVERKD  60
   61 DDDKDENFRK FIITSKFPKN VKLAESMLLK NLNTEIEKRE NYKRKLEAAE GDATVVTERS 120
  121 DSASFLEEKE EPQENHDNKE EQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
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: