Protein Info for Sama_0093 in Shewanella amazonensis SB2B

Annotation: DNA-directed DNA polymerase (RefSeq)

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 923 PF02739: 5_3_exonuc_N" amino acids 9 to 170 (162 residues), 201.5 bits, see alignment E=1.9e-63 TIGR00593: DNA polymerase I" amino acids 9 to 923 (915 residues), 938.5 bits, see alignment E=2.5e-286 PF01367: 5_3_exonuc" amino acids 171 to 272 (102 residues), 90.5 bits, see alignment E=2e-29 PF01612: DNA_pol_A_exo1" amino acids 324 to 510 (187 residues), 134.3 bits, see alignment E=1e-42 PF22619: DNA_polI_exo1" amino acids 397 to 478 (82 residues), 47.6 bits, see alignment E=3.9e-16 PF00476: DNA_pol_A" amino acids 546 to 920 (375 residues), 549 bits, see alignment E=1.4e-168

Best Hits

Swiss-Prot: 67% identical to DPO1_ECOLI: DNA polymerase I (polA) from Escherichia coli (strain K12)

KEGG orthology group: K02335, DNA polymerase I [EC: 2.7.7.7] (inferred from 67% identity to ebw:BWG_3534)

MetaCyc: 67% identical to DNA polymerase I (Escherichia coli K-12 substr. MG1655)
3.1.11.-; 3.1.11.-; DNA-directed DNA polymerase. [EC: 2.7.7.7]

Predicted SEED Role

"DNA polymerase I (EC 2.7.7.7)" in subsystem DNA-replication or DNA Repair Base Excision (EC 2.7.7.7)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 2.7.7.7

Use Curated BLAST to search for 2.7.7.7

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Compare to protein structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

See A1S1P9 at UniProt or InterPro

Protein Sequence (923 amino acids)

>Sama_0093 DNA-directed DNA polymerase (RefSeq) (Shewanella amazonensis SB2B)
MPDIASNPLILVDGSSYLYRAYYAPPHLTNSKGEATGAVYGVVNMLRSLLSRYRPTQMAV
VFDAKGPTFRNEMYQEYKAHRPPMPDDLRSQIAPLHRIIKALGIPLISIPGVEADDVIGT
IAIQAGNEGRSVLISTGDKDMAQLVNEHITLINTMTDTILGPEEVATKFGVGPELIIDLL
AMMGDKADNIPGLPGVGEKTALAMLTGAGGVAKLLAEPDCVTDLGFRGAKTMAAKIRDNA
EMLELSYKLATIKTDVTLEQDWHQLSLSEPNRDELIACYGEMEFKRWLAEVLDNKSPLGT
KAAAPQANQETTESPAAAVIETQYHTLLTESELDAWLDKLSKAELIAVDTETTSLDYMQA
ELVGLSFAIEAGKAAYLPLGHDYPGAPSQLPREATLAKLKPLLENPDIKKVGQNLKYDMS
VLANAGIQLKGVAFDTMLESYVFNSVASRHDMDGLALKYLGHKNISFEEIAGKGAKQLTF
NQIALEQAAPYAAEDADITLRLHQHLWPRLSKEEGLESVFTELELPLIEVLSDIERRGVL
IDSMLLGQQSEELARKIDELEQHAHEIAGEPFNLSSTKQLQELFFTKLGYPVIKKTPKGA
PSTAEEVLVELALDYPLPKIILEHRSLTKLKSTYTDKLPLMINGRTGRVHTSYHQANAAT
GRLSSSDPNLQNIPIRTEEGRRIRQAFVAPEGKRILAADYSQIELRIMAHLSQDEGLLRA
FAEGKDIHRATAAEVFDVAFETVTSEQRRRAKAVNFGLIYGMSAFGLARQLDIPRNEAQS
YIDTYFKRYPGVLKYMEETRAMASEQGYVSTLFGRRLYLPEIRDRNAMRRQAAERAAINA
PMQGTAADIIKKAMIAIQHWIKTETQGEIQMIMQVHDELVFEVDADKADALKEKVCELMA
AAASLDVPLLAEAGLGDNWDQAH