YRC Public Data Repository - Protein Structure Prediction

Protein:	SKI6
Organism:	Saccharomyces cerevisiae
Length:	246 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 SKI6.

Description	E-value	Query Range	Subject Range
PNP_BACSU - Polyribonucleotide nucleotidyltransferase OS=Bacillus subtilis GN=pnp PE=1 SV=3 gi\|221313871 - gi\|221313871\|ref\|ZP_03595676.1\| polynucleotide phosphorylase/polyadenylase [Bacillus subtilis subsp.... gi\|221318794 - gi\|221318794\|ref\|ZP_03600088.1\| polynucleotide phosphorylase/polyadenylase [Bacillus subtilis subsp.... gi\|221323066 - gi\|221323066\|ref\|ZP_03604360.1\| polynucleotide phosphorylase/polyadenylase [Bacillus subtilis subsp.... PNP_BACSU - Polyribonucleotide nucleotidyltransferase OS=Bacillus subtilis (strain 168) GN=pnp PE=1 SV=3	2.0E-70	[5..245]	[308..555]
PNP_BACHD - Polyribonucleotide nucleotidyltransferase OS=Bacillus halodurans GN=pnp PE=3 SV=1 PNP_BACHD - Polyribonucleotide nucleotidyltransferase OS=Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / ...	2.0E-69	[5..245]	[306..553]
gi\|221142508 - gi\|221142508\|ref\|ZP_03567001.1\| polynucleotide phosphorylase/polyadenylase [Staphylococcus aureus su... PNP_STAA2 - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain JH1) GN=pnp PE=3 SV=1 PNP_STAAN - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain N315) GN=pnp PE=1 SV=1 gi\|269202891\|ref... - polynucleotide phosphorylase/polyadenylase [Staphylococcus aureus subsp. aureus ED98] gi\|25311828 - pir\|\|E89901 polyribonucleotide nucleotidyltransferase [imported] - Staphylococcus aureus (strain N31... PNP_STAAM - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=pn... PNP_STAA1 - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=pnp... PNP_STAAT - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain USA300 / TCH1516) GN=pnp ... PNP_STAAE - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain Newman) GN=pnp PE=3 SV=1 PNP_STAA9 - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain JH9) GN=pnp PE=3 SV=1 PNP_STAA8 - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain NCTC 8325) GN=pnp PE=1 SV... PNP_STAA3 - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain USA300) GN=pnp PE=3 SV=1 PNP_STAAC - Polyribonucleotide nucleotidyltransferase OS=Staphylococcus aureus (strain COL) GN=pnp PE=3 SV=1 gi\|253316410 - gi\|253316410\|ref\|ZP_04839623.1\| polynucleotide phosphorylase/polyadenylase [Staphylococcus aureus su... gi\|253728542, gi... - gi\|253733488\|ref\|ZP_04867653.1\| polynucleotide phosphorylase/polyadenylase [Staphylococcus aureus su... gi\|255006061 - gi\|255006061\|ref\|ZP_05144662.2\| polynucleotide phosphorylase/polyadenylase [Staphylococcus aureus su... gi\|87126844\|gb\|A... - polyribopolyribonucleotide nucleotidyltransferase [Staphylococcus aureus subsp. aureus USA300], poly...	7.0E-69	[5..245]	[311..558]
PNP_THET2 - Polyribonucleotide nucleotidyltransferase OS=Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM ... PNP_THETH - Polyribonucleotide nucleotidyltransferase OS=Thermus thermophilus GN=pnp PE=3 SV=1	1.0E-68	[5..245]	[319..566]
PNP_LISIN - Polyribonucleotide nucleotidyltransferase OS=Listeria innocua serovar 6a (strain CLIP 11262) GN=pnp ... PNP_LISIN - Polyribonucleotide nucleotidyltransferase OS=Listeria innocua GN=pnp PE=3 SV=1	2.0E-68	[5..245]	[309..556]
gi\|47015662, gi\|... - gi\|47095916\|ref\|ZP_00233519.1\| polyribonucleotide nucleotidyltransferase [Listeria monocytogenes str... PNP_LISMO - Polyribonucleotide nucleotidyltransferase OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-67... PNP_LISMO - Polyribonucleotide nucleotidyltransferase OS=Listeria monocytogenes GN=pnp PE=3 SV=1 gi\|153183693, gi... - gi\|254898504\|ref\|ZP_05258428.1\| polynucleotide phosphorylase/polyadenylase [Listeria monocytogenes J... gi\|127765716, gi... - gi\|254912005\|ref\|ZP_05262017.1\| polynucleotide phosphorylase/polyadenylase [Listeria monocytogenes J... gi\|153174411, gi... - gi\|254827592\|ref\|ZP_05232279.1\| polynucleotide phosphorylase/polyadenylase [Listeria monocytogenes F... gi\|224501726 - gi\|224501726\|ref\|ZP_03670033.1\| polynucleotide phosphorylase/polyadenylase [Listeria monocytogenes F... gi\|254936332, gi... - gi\|254936332\|ref\|ZP_05268029.1\| polynucleotide phosphorylase/polyadenylase [Listeria monocytogenes F...	3.0E-68	[5..245]	[309..556]
PNP_RALSO - Polyribonucleotide nucleotidyltransferase OS=Ralstonia solanacearum GN=pnp PE=3 SV=1 PNP_RALSO - Polyribonucleotide nucleotidyltransferase OS=Ralstonia solanacearum (strain GMI1000) GN=pnp PE=3 SV=...	6.0E-68	[7..245]	[309..554]
gi\|107103839 - gi\|107103839\|ref\|ZP_01367757.1\| hypothetical protein PaerPA_01004910 [Pseudomonas aeruginosa PACS2] gi\|84317379, gi\|... - gi\|84317379\|ref\|ZP_00965827.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... gi\|194555343, gi... - gi\|84323603\|ref\|ZP_00971672.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_PSEAB - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas aeruginosa (strain UCBPP-PA14) GN=pnp PE=3 ... PNP_PSEAE - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C /... PNP_PSEAE - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas aeruginosa GN=pnp PE=3 SV=1 PNP_PSEA8 - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas aeruginosa (strain LESB58) GN=pnp PE=3 SV=1	9.0E-68	[5..244]	[308..554]
PNP_THESQ - Polyribonucleotide nucleotidyltransferase OS=Thermotoga sp. (strain RQ2) GN=pnp PE=3 SV=1 PNP_THEMA - Polyribonucleotide nucleotidyltransferase OS=Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 310... PNP_THEMA - Polyribonucleotide nucleotidyltransferase OS=Thermotoga maritima GN=pnp PE=3 SV=1	1.0E-67	[5..244]	[309..555]
PNP_PSEPU - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas putida GN=pnp PE=3 SV=1	3.0E-67	[5..244]	[308..554]

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Predicted Domain #1

Region A:
Residues: [1-23]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSRLEIYSPE GLRLDGRRWN ELR

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [160-223]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GISVGLYDTT PLLDTNSLEE NAMSTVTLGV VGKSEKLSLL LVEDKIPLDR LENVLAIGIA  60
   61 GAHR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	55.69897
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
exoribonuclease activity	7.55877202113513	bayes_pls_golite062009
ribonuclease activity	7.54644729272203	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	7.5310318714913	bayes_pls_golite062009
3'-5'-exoribonuclease activity	6.46930372693262	bayes_pls_golite062009
3'-5' exonuclease activity	4.29895100594643	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	3.83939403332553	bayes_pls_golite062009
exonuclease activity	3.40686901061667	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.86434572018929	bayes_pls_golite062009
RNA binding	2.05527376734941	bayes_pls_golite062009
structural constituent of ribosome	1.90115575554186	bayes_pls_golite062009
structural molecule activity	1.69321127364043	bayes_pls_golite062009
hydrolase activity	1.55476709794855	bayes_pls_golite062009
binding	1.3018457178158	bayes_pls_golite062009
transcription regulator activity	1.20748032530392	bayes_pls_golite062009
mRNA binding	1.17402119891853	bayes_pls_golite062009
nucleic acid binding	1.05662964529454	bayes_pls_golite062009
catalytic activity	0.878454819018611	bayes_pls_golite062009
DNA binding	0.828609700556836	bayes_pls_golite062009
nuclease activity	0.69721312877891	bayes_pls_golite062009
carbohydrate kinase activity	0.51810239718467	bayes_pls_golite062009
tRNA-specific ribonuclease activity	0.383567539949931	bayes_pls_golite062009
ATP-dependent peptidase activity	0.1173709890655	bayes_pls_golite062009
protein binding	0.0913090112555771	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0287026367466632	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [24-159]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RFESSINTHP HAADGSSYME QGNNKIITLV KGPKEPRLKS QMDTSKALLN VSVNITKFSK  60
   61 FERSKSSHKN ERRVLEIQTS LVRMFEKNVM LNIYPRTVID IEIHVLEQDG GIMGSLINGI 120
  121 TLALIDAGIS MFDYIS

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [224-246]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VRDLMDEELR KHAQKRVSNA SAR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	55.69897
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: