YRC Public Data Repository - Protein Structure Prediction

Protein:	DPO3_STRPN
Organism:	Streptococcus pneumoniae
Length:	1463 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 DPO3_STRPN.

Description	E-value	Query Range	Subject Range
DPO3_STRR6 - DNA polymerase III PolC-type OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) GN=polC PE=3 SV=... DPO3_STRP2 - DNA polymerase III PolC-type OS=Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) GN=polC... gi\|25312571 - pir\|\|C97903 DNA-directed DNA polymerase (EC 2.7.7.7) III, alpha chain [imported] - Streptococcus pne...	1338.0	[0..1]	[1463..1]
gi\|77409408, gi\|... - gi\|77409408\|ref\|ZP_00786106.1\| DNA polymerase III, alpha subunit, Gram-positive type [Streptococcus ...	1311.0	[0..1]	[1463..1]
DPO3_STRMU - DNA polymerase III polC-type OS=Streptococcus mutans GN=polC PE=3 SV=1 DPO3_STRMU - DNA polymerase III PolC-type OS=Streptococcus mutans serotype c (strain ATCC 700610 / UA159) GN=polC...	1311.0	[0..1]	[1463..1]
gi\|77405656, gi\|... - gi\|77405656\|ref\|ZP_00782744.1\| DNA polymerase III, alpha subunit, Gram-positive type [Streptococcus ...	1311.0	[0..1]	[1463..1]
gi\|76787214, gi\|... - gi\|76787214\|ref\|YP_330464.1\| DNA polymerase III PolC [Streptococcus agalactiae A909], gi\|76562271\|gb...	1311.0	[0..1]	[1463..1]
DPO3_STRA5 - DNA polymerase III polC-type OS=Streptococcus agalactiae serotype V GN=polC PE=3 SV=1 DPO3_STRA3 - DNA polymerase III polC-type OS=Streptococcus agalactiae serotype III GN=polC PE=3 SV=1 DPO3_STRA5 - DNA polymerase III PolC-type OS=Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)... gi\|76798733, gi\|... - gi\|76798733\|ref\|ZP_00780952.1\| DNA polymerase III, alpha subunit, Gram-positive type [Streptococcus ... DPO3_STRA3 - DNA polymerase III PolC-type OS=Streptococcus agalactiae serotype III (strain NEM316) GN=polC PE=3 S...	1310.0	[0..1]	[1463..1]
gi\|77161647, gi\|... - gi\|77412300\|ref\|ZP_00788615.1\| DNA polymerase III, alpha subunit, Gram-positive type [Streptococcus ...	1309.0	[0..1]	[1463..1]
DPO3_BACSU - DNA polymerase III polC-type OS=Bacillus subtilis GN=polC PE=1 SV=2 gi\|221318783 - gi\|221318783\|ref\|ZP_03600077.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. JH64... gi\|221313860 - gi\|221313860\|ref\|ZP_03595665.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. NCIB... gi\|221323055 - gi\|221323055\|ref\|ZP_03604349.1\| DNA polymerase III PolC [Bacillus subtilis subsp. subtilis str. SMY] DPO3_BACSU - DNA polymerase III PolC-type OS=Bacillus subtilis (strain 168) GN=polC PE=1 SV=2	1306.0	[0..4]	[1459..10]
gi\|48824832 - ref\|ZP_00286162.1\| COG2176: DNA polymerase III, alpha subunit (gram-positive type) [Enterococcus fae... gi\|68195041, gi\|... - gi\|69246860\|ref\|ZP_00604152.1\| DNA polymerase III, epsilon subunit:DNA polymerase III, alpha subunit...	1305.0	[0..1]	[1462..1]
gi\|228660107, gi... - gi\|229123331\|ref\|ZP_04252535.1\| DNA polymerase III polC-type [Bacillus cereus 95/8201], gi\|228660107... gi\|21401801, gi\|... - gi\|65321145\|ref\|ZP_00394104.1\| COG2176: DNA polymerase III, alpha subunit (gram-positive type) [Baci... gi\|228947537, gi... - gi\|228947537\|ref\|ZP_04109827.1\| DNA polymerase III polC-type [Bacillus thuringiensis serovar monterr... gi\|227813274, gi... - gi\|227813274\|ref\|YP_002813283.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus ant... gi\|165872624, gi... - gi\|165872624\|ref\|ZP_02217255.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|170687849, gi... - gi\|170687849\|ref\|ZP_02879063.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|170128318, gi... - gi\|170706900\|ref\|ZP_02897358.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|49180595, gi\|... - gi\|49186668\|ref\|YP_029920.1\| DNA polymerase III PolC [Bacillus anthracis str. Sterne], gi\|49180595\|g... gi\|52141670, gi\|... - gi\|52141670\|ref\|YP_085159.1\| DNA polymerase III PolC [Bacillus cereus E33L], gi\|51975139\|gb\|AAU16689... gi\|30258465, gi\|... - gi\|30263821\|ref\|NP_846198.1\| DNA polymerase III PolC [Bacillus anthracis str. Ames], gi\|30258465\|gb\|... gi\|47504393, gi\|... - gi\|47529245\|ref\|YP_020594.1\| DNA polymerase III PolC [Bacillus anthracis str. 'Ames Ancestor'], gi\|4... gi\|190568456, gi... - gi\|190568456\|ref\|ZP_03021363.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus anth... gi\|196042171, gi... - gi\|196042171\|ref\|ZP_03109454.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus cere... gi\|218904946, gi... - gi\|218904946\|ref\|YP_002452780.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus cer... gi\|254759330 - gi\|254759330\|ref\|ZP_05211355.1\| DNA polymerase III PolC [Bacillus anthracis str. Australia 94] gi\|254756009 - gi\|254756009\|ref\|ZP_05208040.1\| DNA polymerase III PolC [Bacillus anthracis str. Vollum] gi\|254721996 - gi\|254721996\|ref\|ZP_05183785.1\| DNA polymerase III PolC [Bacillus anthracis str. A1055] gi\|254683475 - gi\|254683475\|ref\|ZP_05147335.1\| DNA polymerase III PolC [Bacillus anthracis str. CNEVA-9066] gi\|229601637, gi... - gi\|229601637\|ref\|YP_002868056.1\| DNA polymerase III, alpha subunit, Gram-positive type [Bacillus ant...	1302.0	[0..2]	[1459..8]

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Predicted Domain #1

Region A:
Residues: [1-332]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSNSFEILMN QLGMPAEMRQ APALAQANIE RVVVHKISKV WEFHFVFSNI LPIEIFLELK  60
   61 KGLSEEFSKT GNKAVFEIKA RSQEFSNQLL QSYYREAFSE GPCASQGFKS LYQNLQVRAE 120
  121 GNQLFIEGSE AIDKEHFKKN HLPNLAKQLE KFGFPTFNCQ VEKNDVLTQE QEEAFHAENE 180
  181 QIVQAANEEA LRAMEQLEQM APPPAEEKPA FDFQAKKAAA KPKLDKAEIT PMIEVTTEEN 240
  241 RLVFEGVVFD VEQKVTRTGR VLINFKMTDY TSSFSMQKWV KNEEEAQKFD LIKKNSWLRV 300
  301 RGNVEMNNFT RDLTMNVQDL QEVVHYERKD LM

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.30103
Match:	2fkjA
Description:	No description for 2fkjA was found.

Predicted Domain #2

Region A:
Residues: [333-432]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PEGERRVEFH AHTNMSTMDA LPEVEEIVAT AAKWGHKAVA ITDHGNVQSF PHGYKAAKKA  60
   61 GIQLIYGMEA NIVEDRVPIV YNEVEMDLSE ATYVVFDVET

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	3.05
Match:	1m65A
Description:	Hypothetical protein YcdX
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [433-533]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TGLSAIYNDL IQVAASKMYK GNVIAEFDEF INPGHPLSAF TTELTGITDD HVKNAKPLEQ  60
   61 VLQEFQEFCK DTVLVAHNAT FDVGFMNANY ERHDLPKISQ P

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.39794
Match:	2guiA
Description:	No description for 2guiA was found.

Predicted functions:

Term	Confidence	Notes
DNA polymerase activity	7.87431862983329	bayes_pls_golite062009
DNA-directed DNA polymerase activity	7.78411937387917	bayes_pls_golite062009
nucleotidyltransferase activity	5.3880945520411	bayes_pls_golite062009
exonuclease activity	2.86892175148145	bayes_pls_golite062009
nuclease activity	2.84202779131927	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	1.94077739152313	bayes_pls_golite062009
deoxyribonuclease activity	1.87431870698721	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.87430802282815	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.75713164321634	bayes_pls_golite062009
transferase activity	1.47288345517763	bayes_pls_golite062009
ribonuclease activity	1.41871623152578	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
endonuclease activity	0.935348031740788	bayes_pls_golite062009
exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.782108781904855	bayes_pls_golite062009
exodeoxyribonuclease activity	0.77421125364834	bayes_pls_golite062009
3'-5' exonuclease activity	0.64268174969672	bayes_pls_golite062009
endodeoxyribonuclease activity	0.48776342704945	bayes_pls_golite062009
exoribonuclease activity	0.26279899872348	bayes_pls_golite062009
nucleic acid binding	0.251640316483416	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.18445559832317	bayes_pls_golite062009
single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	0.1355017328177	bayes_pls_golite062009
binding	0.122249780594036	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [534-1463]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VIDTLEFARN LYPEYKRHGL GPLTKRFGVA LEHHHMANYD AEATGRLLFI FIKEVAEKHG  60
   61 VTDLARLNID LISPDSYKKA RIKHATIYVK NQVGLKNIFK LVSLSNTKYF EGVPRIPRTV 120
  121 LDAHREGLIL GSACSEGEVF DVVVSQGVDA AVEVAKYYDF IEVMPPAIYA PLIAKEQVKD 180
  181 MEELQTIIKS LIEVGDRLGK PVLATGNVHY IEPEEEIYRE IIVRSLGQGA MINRTIGHGE 240
  241 HAQPAPLPKA HFRTTNEMLD EFAFLGEELA RKLVIENTNA LAEIFESVEV VKGDLYTPFI 300
  301 DKAEETVAEL TYKKAFEIYG NPLPDIVDLR IEKELTSILG NGFAVIYLAS QMLVQRSNER 360
  361 GYLVGSRGSV GSSFVATMIG ITEVNPLSPH YVCGQCQYSE FITDGSYGSG FDMPHKDCPN 420
  421 CGHKLSKNGQ DIPFETFLGF DGDKVPDIDL NFSGEDQPSA HLDVRDIFGE EYAFRAGTVG 480
  481 TVAAKTAYGF VKGYERDYGK FYRDAEVERL AQGAAGVKRT TGQHPGGIVV IPNYMDVYDF 540
  541 TPVQYPADDV TAEWQTTHFN FHDIDENVLK LDVLGHDDPT MIRKLQDLSG IDPNKIPMDD 600
  601 EGVMALFSGT DVLGVTPEQI GTPTGMLGIP EFGTNFVRGM VDETHPTTFA ELLQLSGLSH 660
  661 GTDVWLGNAQ DLIKQGIADL STVIGCRDDI MVYLMHAGLE PKMAFTIMER VRKGLWLKIS 720
  721 EEERNGYIEA MKANKVPEWY IESCGKIKYM FPKAHAAAYV MMALRVAYFK VHHPIYYYCA 780
  781 YFSIRAKAFD IKTMGAGLEV IKRRMEEISE KRKNNEASNV EIDLYTTLEI VNEMWERGFK 840
  841 FGKLDLYCSQ ATEFLIDGDT LIPPFVAMDG LGENVAKQLV RAREEGEFLS KTELRKRGGL 900
  901 SSTLVEKMDE MGILGNMPED NQLSLFDELF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.0
Match:	2hnhA
Description:	No description for 2hnhA was found.

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: