YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24372461, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	438 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 gi|24372461, gi|....

Description	E-value	Query Range	Subject Range
gi\|37680945, gi\|... - gi\|37680945\|ref\|NP_935554.1\| polyA polymerase [Vibrio vulnificus YJ016], gi\|37199695\|dbj\|BAC95525.1\|...	454.0	[0..1]	[437..29]
gi\|27361153, gi\|... - gi\|27365007\|ref\|NP_760535.1\| tRNA nucleotidyltransferase/poly(A) polymerase [Vibrio vulnificus CMCP6...	452.0	[0..1]	[437..21]
gi\|16763574, gi\|... - gi\|16763574\|ref\|NP_459189.1\| poly(A) polymerase I [Salmonella typhimurium LT2], gi\|16418686\|gb\|AAL19... lcl\|NC_016856.1_... - [gene=pcnB] [protein=poly(A) polymerase I] [protein_id=YP_005235849.1] [location=complement(214578..... PCNB_SALTY - (Q8ZRQ8) Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein)	440.0	[0..1]	[413..36]
gi\|62178754, gi\|... - gi\|62178754\|ref\|YP_215171.1\| poly(A) polymerase I [Salmonella enterica subsp. enterica serovar Chole... gi\|224582031, gi... - gi\|224582031\|ref\|YP_002635829.1\| polyA polymerase I [Salmonella enterica subsp. enterica serovar Par... gi\|206707503, gi... - gi\|207855700\|ref\|YP_002242351.1\| poly(A) polymerase I [Salmonella enterica subsp. enterica serovar E... gi\|205271304, gi... - gi\|205351523\|ref\|YP_002225324.1\| poly(A) polymerase I [Salmonella enterica subsp. enterica serovar G...	440.0	[0..1]	[413..36]
PCNB_SALTY - Poly(A) polymerase OS=Salmonella typhimurium GN=pcnB PE=3 SV=2 PCNB_SALTY - Poly(A) polymerase OS=Salmonella typhimurium GN=pcnB PE=3 SV=2 PCNB_SALTY - Poly(A) polymerase I OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=pcnB PE=3 SV...	440.0	[0..1]	[413..29]
gi\|197361396, gi... - gi\|197361396\|ref\|YP_002141031.1\| poly(A) polymerase I [Salmonella enterica subsp. enterica serovar P... gi\|56412460, gi\|... - gi\|56412460\|ref\|YP_149535.1\| poly(A) polymerase I [Salmonella enterica subsp. enterica serovar Parat...	439.0	[0..1]	[413..36]
PCNB_ECOL6 - (P0ABF2) Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein) gi\|82542743, gi\|... - gi\|82542743\|ref\|YP_406690.1\| poly(A) polymerase I [Shigella boydii Sb227], gi\|81244154\|gb\|ABB64862.1... gi\|209917334, gi... - gi\|209917334\|ref\|YP_002291418.1\| poly(A) polymerase I [Escherichia coli SE11], gi\|209910593\|dbj\|BAG7... gi\|162139816 - gi\|162139816\|ref\|NP_308174.2\| poly(A) polymerase I [Escherichia coli O157:H7 str. Sakai] gi\|161986592 - gi\|161986592\|ref\|YP_309183.2\| poly(A) polymerase I [Shigella sonnei Ss046] tr\|A0A0G3HX71\|A0... - Poly(A) polymerase I OS=Escherichia coli (strain K12) GN=pcnB PE=3 SV=2 gi\|26246087, gi\|... - gi\|26246087\|ref\|NP_752126.1\| poly(A) polymerase I [Escherichia coli CFT073], gi\|26106484\|gb\|AAN78670... PCNB_ECO57 - (P0ABF3) Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein) gi\|218368550, gi... - gi\|218698564\|ref\|YP_002406193.1\| poly(A) polymerase I [Escherichia coli IAI39], gi\|218368550\|emb\|CAR... gi\|218688020, gi... - gi\|218688020\|ref\|YP_002396232.1\| poly(A) polymerase I [Escherichia coli ED1a], gi\|218425584\|emb\|CAR0... gi\|218363855, gi... - gi\|218557086\|ref\|YP_002389999.1\| poly(A) polymerase I [Escherichia coli S88], gi\|218363855\|emb\|CAR01... gi\|254037561, gi... - gi\|254037561\|ref\|ZP_04871638.1\| poly(A) polymerase I [Escherichia sp. 1_1_43], gi\|226840667\|gb\|EEH72... PCNB_ECOLI - (P0ABF1) Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein) gi\|226902214, gi... - gi\|237704302\|ref\|ZP_04534783.1\| poly(A) polymerase I [Escherichia sp. 3_2_53FAA], gi\|226902214\|gb\|EE... gi\|110341956, gi... - gi\|110640364\|ref\|YP_668092.1\| poly(A) polymerase I [Escherichia coli 536], gi\|110341956\|gb\|ABG68193....	438.0	[0..1]	[412..36]
gi\|30039945, gi\|... - gi\|30061703\|ref\|NP_835874.1\| poly(A) polymerase I [Shigella flexneri 2a str. 2457T], gi\|30039945\|gb\|... gi\|56383162, gi\|... - gi\|56479611\|ref\|NP_706091.2\| poly(A) polymerase I [Shigella flexneri 2a str. 301], gi\|56383162\|gb\|AA...	438.0	[0..1]	[412..18]
gi\|254791278, gi... - gi\|254791278\|ref\|YP_003076115.1\| poly(A) polymerase I [Escherichia coli O157:H7 str. TW14359], gi\|25... gi\|238862072, gi... - gi\|238899542\|ref\|YP_002925338.1\| poly(A) polymerase I [Escherichia coli BW2952], gi\|238862072\|gb\|ACR... gi\|85674351, gi\|... - gi\|89107024\|ref\|AP_000804.1\| poly(A) polymerase I [Escherichia coli str. K-12 substr. W3110], gi\|856... EG10690 - poly(A) polymerase / Poly(A) polymerase; controls plasmid copy number; rare AUU start codon, growth-... PCNB_ECO57 - Poly(A) polymerase I OS=Escherichia coli O157:H7 GN=pcnB PE=3 SV=2 PCNB_ECOL6 - Poly(A) polymerase OS=Escherichia coli O6 GN=pcnB PE=3 SV=2 EG10690 - poly(A) polymerase / Poly(A) polymerase; controls plasmid copy number; rare AUU start codon, growth-... gi\|170079780, gi... - gi\|170079780\|ref\|YP_001729100.1\| poly(A) polymerase I [Escherichia coli str. K-12 substr. DH10B], gi... PCNB_ECOLI - Poly(A) polymerase (EC 2.7.7.19) (PAP) (Plasmid copy number protein) - Escherichia coli PCNB_ECOL6 - Poly(A) polymerase I OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=pcnB PE=3 SV=...	438.0	[0..1]	[412..29]
gi\|46156358, gi\|... - gi\|46156358\|ref\|ZP_00204685.1\| COG0617: tRNA nucleotidyltransferase/poly(A) polymerase [Haemophilus ...	438.0	[0..3]	[430..24]

Back

Predicted Domain #1

Region A:
Residues: [1-356]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALVPRDAHS ISRKQISENA LKVLYRLNKA GFQAYLVGGG VRDLLLGLEP KDFDVVTNAT  60
   61 PEEIKKLFRN CRVVGRRFRL AHIVFGRDVI EVATFRGHHG ESNEKISKAN AEGRLLRDNV 120
  121 YGEIDEDAER RDFTVNALYY DISDYSIRSY GGGMEDLKAG TLRLIGDPET RYREDPVRML 180
  181 RAVRFATKLS MTIDEVTAKP IKQLAPLLKD IPAARMYEEV LKLFFAGKAV ANFDMMQEYK 240
  241 LFAPLFPQVD ALLKEAPKGP AMKMVQAIMK STDDRVNEDK PVTPSFFYAA ILWYPLRQRA 300
  301 EDIAVESGLT LYDAFFAAMG DVMEQQCQTI SIPRRFSTPA KDIWQLQLRF ERSQGT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	71.0
Match:	1mivA
Description:	tRNA CCA-adding enzyme, C-terminal domains; tRNA CCA-adding enzyme, head domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transferase activity, transferring phosphorus-containing groups	2.13977436268217	bayes_pls_golite062009
RNA binding	1.95446539797934	bayes_pls_golite062009
transferase activity	1.58185056077551	bayes_pls_golite062009
nucleotidyltransferase activity	1.28424599869932	bayes_pls_golite062009
catalytic activity	0.75232920999699	bayes_pls_golite062009
polynucleotide adenylyltransferase activity	0.747086661208511	bayes_pls_golite062009
tRNA binding	0.671378805940772	bayes_pls_golite062009
nucleic acid binding	0.56250895409788	bayes_pls_golite062009
binding	0.248197954076327	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [357-438]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RAFKLLEHPK FRAAYDLLLL RGEVEGGNLA KSAAWWQQFV EADETERLTI ARSGNKASGN  60
   61 RNRNTPQRRR RRPSGAKAKA EE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident 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: