Protein Info for PP_0123 in Pseudomonas putida KT2440

Annotation: DNA polymerase I, 5

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 915 TIGR00593: DNA polymerase I" amino acids 6 to 915 (910 residues), 937.1 bits, see alignment E=6.7e-286 PF02739: 5_3_exonuc_N" amino acids 6 to 167 (162 residues), 179.2 bits, see alignment E=1.4e-56 PF01367: 5_3_exonuc" amino acids 168 to 271 (104 residues), 100.1 bits, see alignment E=2e-32 PF01612: DNA_pol_A_exo1" amino acids 314 to 502 (189 residues), 122.5 bits, see alignment E=4.1e-39 PF22619: DNA_polI_exo1" amino acids 388 to 469 (82 residues), 41.1 bits, see alignment E=4e-14 PF00476: DNA_pol_A" amino acids 536 to 913 (378 residues), 544.7 bits, see alignment E=3e-167

Best Hits

Swiss-Prot: 81% identical to DPO1_PSEAE: DNA polymerase I (polA) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K02335, DNA polymerase I [EC: 2.7.7.7] (inferred from 78% identity to avn:Avin_00630)

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 Q88RK6 at UniProt or InterPro

Protein Sequence (915 amino acids)

>PP_0123 DNA polymerase I, 5 (Pseudomonas putida KT2440)
MSQAPLVLVDGSSYLYRAFHALPPLTTSKGMPTGAVKGVLNMLKSLRKQYPDSLFAVVFD
AKGGTFRDAMFAEYKANRPSMPDDLRVQIEPLHASVKALGYPLLCVEGVEADDVIGTLAR
SSAALGRPVIISTGDKDMAQLVDGHITLVNTMTGSVLDVAGVHEKFGVGPEHIIDFLALM
GDKVDNIPGVPGVGEKTAVGLLTGIGGGLSDLYANLDKVPALAIRGAKTLPAKLEEHRDA
AFLSYELATIKVDVPLDVEVEALVCGEPDREALLALYTEMEFKSWVAELQRDAAKAGDDV
APAVEPAVKVEAKYETILDQARFDAWLEKLRQAPLFAFDTETTGLDAQQAQLVGLSFAVE
PHEAAYVPLAHDYEGAPVQLDREAVLLALKPLLEDPAKAKVGQNAKYDINILANGSPAIE
MRGVAYDTMLESYVLNSTATRHDMDSLAQKYLDHTTIAFEDIAGKGAKQLTFNQINLDKA
GPYAAEDADITLRLHHALQARLAQTPSVQPVLMDIEMPLVPVLARIERQGALVDAELLKV
QSGELGVKMAELELRAYELAGETFNLGSPKQLGTILYDKLGMPVLSKTAKGQPSTAEAVL
DELALQGYPLPEVLMQYRSLSKLKSTYTDKLPGQINPRTGRIHTSYQQAVAATGRLSSSD
PNLQNIPIRTAEGRRIRQAFIASPGYKLLAADYSQIELRIMAHLAKDEGLLHAFRNDLDV
HRATAAEVFGVALEDVTTDQRRSAKAINFGLIYGMSAFGLAKQIGVDRKQSQDYIDRYFA
RYPGVLAYMERTRAQAAEQGFVETLFGRRLYLPDINAKNPALRKGAERTAINAPMQGTAA
DIIKRAMVKVDNWLSESGLDARVILQVHDELVLEVREDLVQQVKDEIRQHMSQAAQLDVP
LLVEAGVGANWDEAH