YRC Public Data Repository - Protein Structure Prediction

Protein:	RRP46
Organism:	Saccharomyces cerevisiae
Length:	256 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 RRP46.

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	6.0E-63	[8..252]	[300..548]
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-61	[8..252]	[298..546]
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...	1.0E-60	[8..252]	[303..551]
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	5.0E-60	[9..255]	[302..558]
gi\|7473346 - pir\|\|G75320 polynucleotide phosphorylase - Deinococcus radiodurans (strain R1) gi\|6459851, gi\|1... - gi\|6459851\|gb\|AAF11608.1\|AE002042_3 polynucleotide phosphorylase [Deinococcus radiodurans R1], gi\|15...	5.0E-60	[3..252]	[329..582]
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...	1.0E-59	[9..255]	[302..558]
PNP_PSEPU - Polyribonucleotide nucleotidyltransferase OS=Pseudomonas putida GN=pnp PE=3 SV=1	2.0E-59	[3..252]	[295..548]
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	3.0E-59	[6..252]	[309..559]
PNP_BUCAI - Polyribonucleotide nucleotidyltransferase OS=Buchnera aphidicola subsp. Acyrthosiphon pisum GN=pnp P... PNP_BUCAT - Polyribonucleotide nucleotidyltransferase OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain ... PNP_BUCA5 - Polyribonucleotide nucleotidyltransferase OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain ... gi\|311087269\|gb\|... - polynucleotide phosphorylase/polyadenylase [Buchnera aphidicola str. JF99 (Acyrthosiphon pisum)] gi\|25311798 - gi\|25311798\|pir\|\|E84973 polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) [imported] - Buchnera... PNP_BUCAI - Polyribonucleotide nucleotidyltransferase OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain ... gi\|311086683\|gb\|... - polynucleotide phosphorylase/polyadenylase [Buchnera aphidicola str. TLW03 (Acyrthosiphon pisum)] gi\|257471431\|ref... - polynucleotide phosphorylase/polyadenylase [Buchnera aphidicola str. LSR1 (Acyrthosiphon pisum)] gi\|209570527\|emb... - unnamed protein product [Buchnera aphidicola] gi\|311086110\|gb\|... - polynucleotide phosphorylase/polyadenylase [Buchnera aphidicola str. LL01 (Acyrthosiphon pisum)]	3.0E-59	[6..252]	[297..547]
PNP_BRUME - Polyribonucleotide nucleotidyltransferase OS=Brucella melitensis GN=pnp PE=3 SV=1 PNP_BRUME - Polyribonucleotide nucleotidyltransferase OS=Brucella melitensis biotype 1 (strain 16M / ATCC 23456 ... PNP_BRUMB - Polyribonucleotide nucleotidyltransferase OS=Brucella melitensis biotype 2 (strain ATCC 23457) GN=pn...	3.0E-59	[6..252]	[299..549]

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Predicted Domain #1

Region A:
Residues: [1-34]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNQLRCIKYL CIYGNNKEPN TKNRLDSAEK KKKM

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [166-237]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SIPIAIIKDT SDIIVDPTAE QLKISLSVHT LALEFVNGGK VVKNVLLLDS NGDFNEDQLF  60
   61 SLLELGEQKC QE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.69897
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 Domain #2

Region A:
Residues: [35-165]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SVQAEIGILD HVDGSSEFVS QDTKVICSVT GPIEPKARQE LPTQLALEII VRPAKGVATT  60
   61 REKVLEDKLR AVLTPLITRH CYPRQLCQIT CQILESGEDE AEFSLRELSC CINAAFLALV 120
  121 DAGIALNSMC A

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [238-256]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LVTNIRRIIQ DNISPRLVV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	49.69897
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