YRC Public Data Repository - Protein Structure Prediction

Protein:	PNP_YERPP
Organism:	Yersinia pestis Pestoides F
Length:	705 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 PNP_YERPP.

Description	E-value	Query Range	Subject Range
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	0.0	[1..695]	[1..695]
PNP_ECOL6 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / U... PNP_ECOSM - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=pnp PE=3 S... PNP_ECOUT - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain UTI89 / UPEC) GN=pnp PE=3 SV=2 gi\|237706083, gi... - gi\|237706083\|ref\|ZP_04536564.1\| polynucleotide phosphorylase/polyadenylase [Escherichia sp. 3_2_53FA... gi\|191172253, gi... - gi\|75240811\|ref\|ZP_00724709.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_ECOL6 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O6 GN=pnp PE=3 SV=2 PNP_ECOL5 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=pnp ... PNP_ECOK1 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O1:K1 / APEC GN=pnp PE=3 SV=2 PNP_ECO45 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=pnp PE=... PNP_ECOLU - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN... PNP_ECO81 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O81 (strain ED1a) GN=pnp PE=3 SV=2	0.0	[1..695]	[1..695]
gi\|188495596, gi... - gi\|75513379\|ref\|ZP_00735803.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... gi\|193061952, gi... - gi\|75260094\|ref\|ZP_00731372.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... gi\|75211115, gi\|... - gi\|75211115\|ref\|ZP_00711228.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_ECO24 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=pn... gi\|187775793, gi... - gi\|187775793\|ref\|ZP_02798176.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|189358585, gi... - gi\|189401923\|ref\|ZP_02779152.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|189361407, gi... - gi\|189403294\|ref\|ZP_02794589.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|188024828, gi... - gi\|188024828\|ref\|ZP_02774262.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|189010332, gi... - gi\|189010332\|ref\|ZP_02806314.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... PNP_ECO55 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain 55989 / EAEC) GN=pnp PE=3 SV=2 PNP_ECO57 - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O157:H7 GN=pnp PE=3 SV=2 PNP_ECO7I - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=pnp PE... PNP_ECO5E - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=pnp ... PNP_ECOSE - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain SE11) GN=pnp PE=3 SV=2 gi\|217319969, gi... - gi\|217327602\|ref\|ZP_03443685.1\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... PNP_SHISS - Polyribonucleotide nucleotidyltransferase OS=Shigella sonnei (strain Ss046) GN=pnp PE=3 SV=2 gi\|254594515, gi... - gi\|254795115\|ref\|YP_003079952.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H... gi\|189405568, gi... - gi\|189405568\|ref\|ZP_02822772.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|194417987, gi... - gi\|194433724\|ref\|ZP_03065999.1\| polyribonucleotide nucleotidyltransferase [Shigella dysenteriae 1012... gi\|189367622, gi... - gi\|189404087\|ref\|ZP_02787137.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|189374178, gi... - gi\|189404797\|ref\|ZP_02811056.2\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|208734172, gi... - gi\|208812895\|ref\|ZP_03254224.1\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|208818367, gi... - gi\|208818367\|ref\|ZP_03258687.1\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ... gi\|195938384 - gi\|195938384\|ref\|ZP_03083766.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7... gi\|208729396, gi... - gi\|208809595\|ref\|ZP_03251932.1\| polyribonucleotide nucleotidyltransferase [Escherichia coli O157:H7 ...	0.0	[1..695]	[1..695]
PNP_SHELP - Polyribonucleotide nucleotidyltransferase OS=Shewanella loihica (strain ATCC BAA-1088 / PV-4) GN=pnp...	0.0	[2..701]	[1..700]
PNP_HAEDU - Polyribonucleotide nucleotidyltransferase OS=Haemophilus ducreyi GN=pnp PE=3 SV=1 PNP_HAEDU - Polyribonucleotide nucleotidyltransferase OS=Haemophilus ducreyi (strain 35000HP / ATCC 700724) GN=p...	0.0	[2..695]	[1..694]
PNP_YERPB - Polyribonucleotide nucleotidyltransferase OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+) ... PNP_YERPS - Polyribonucleotide nucleotidyltransferase OS=Yersinia pseudotuberculosis serotype I (strain IP32953)... PNP_YERPS - Polyribonucleotide nucleotidyltransferase OS=Yersinia pseudotuberculosis GN=pnp PE=3 SV=1	0.0	[1..704]	[1..704]
gi\|25311841, gi\|... - pir\|\|AE2586 polyribonucleotide nucleotidyltransferase pnpA [imported] - Agrobacterium tumefaciens (s... PNP_AGRFC - Polyribonucleotide nucleotidyltransferase OS=Agrobacterium fabrum (strain C58 / ATCC 33970) GN=pnp P...	0.0	[1..704]	[1..705]
gi\|192959224, gi... - gi\|75239266\|ref\|ZP_00723237.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph...	0.0	[1..695]	[1..695]
PNP_SHIB3 - Polyribonucleotide nucleotidyltransferase OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512...	0.0	[1..695]	[1..695]
PNP_SHIF8 - Polyribonucleotide nucleotidyltransferase OS=Shigella flexneri serotype 5b (strain 8401) GN=pnp PE=3... PNP_SHIFL - Polyribonucleotide nucleotidyltransferase OS=Shigella flexneri GN=pnp PE=3 SV=5 gi\|75228777, gi\|... - gi\|75228777\|ref\|ZP_00715386.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph...	0.0	[1..695]	[1..695]

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Predicted Domain #1

Region A:
Residues: [1-705]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLTPIIRKFQ YGQHTVTIET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQSFFPLT  60
   61 VNYQERTYAA GRIPGSFFRR EGRPSEGETL TSRLIDRPIR PLFPDSFLNE VQVIATVVSV 120
  121 NPQINPDIVA LIGASAALSL SGIPFNGPIG AARVGFINDQ YVLNPTTDEL KESRLDLVVA 180
  181 GTAGAVLMVE SEADILSEEQ MLGAVVFGHE QQQVVIENIN ALVAEAGKPK WDWQAEPVNE 240
  241 ALHARVAELA EARLGDAYRI TEKQERYTQV DAIKADVTEA LLAQDDTLDA AEIQDILASV 300
  301 EKNVVRSRVL RGEPRIDGRE KDMIRGLDVR TGILPRTHGS ALFTRGETQA LVTATLGTAR 360
  361 DAQNIDELMG ERTDSFLLHY NFPPYCVGET GMVGSPKRRE IGHGRLAKRG VLAVMPSASE 420
  421 FPYTIRVVSE ITESNGSSSM ASVCGASLAL MDAGVPIKAA VAGIAMGLVK EGDNFVVLSD 480
  481 ILGDEDHLGD MDFKVAGSRD GVTALQMDIK IEGITREIMQ VALNQAKGAR LHILGVMEQA 540
  541 ISTPRGDISE FAPRIYTMKI NPEKIKDVIG KGGSVIRALT DETGTTIEIE DDGTIKIAAT 600
  601 DGDKAKHAIR RIEEITAEIE VGRIYAGKVT RIVDFGAFVA IGGGKEGLVH ISQIADKRVE 660
  661 KVTDYLQMGQ DVPVKVMEVD RQGRIRLSIK EATTPDAEAP EAAAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	141.0
Match:	1e3hA
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; 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
ribonuclease activity	3.62650207668685	bayes_pls_golite062009
transcription regulator activity	2.64513435028798	bayes_pls_golite062009
exoribonuclease activity	2.49584565422948	bayes_pls_golite062009
3'-5'-exoribonuclease activity	2.48625785660839	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	2.46667410843173	bayes_pls_golite062009
RNA binding	1.96263727771326	bayes_pls_golite062009
nucleic acid binding	1.06121115244578	bayes_pls_golite062009
transcription termination factor activity	1.01993495617192	bayes_pls_golite062009
binding	0.953779727473657	bayes_pls_golite062009
structural constituent of ribosome	0.82905129800799	bayes_pls_golite062009
ATP-dependent peptidase activity	0.66778558090199	bayes_pls_golite062009
structural molecule activity	0.61730676636766	bayes_pls_golite062009
carbohydrate kinase activity	0.51810239718467	bayes_pls_golite062009
DNA binding	0.42372608430605	bayes_pls_golite062009
	0.416217645025381	bayes_pls_golite062009
hydrolase activity	0.355379071501158	bayes_pls_golite062009
catalytic activity	0.10089766806364	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.0287026367466632	bayes_pls_golite062009

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: