Protein Info for Sama_1154 in Shewanella amazonensis SB2B

Name: dnaE
Annotation: DNA polymerase III subunit alpha (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

1 100 200 300 400 500 600 700 800 900 1000 1100 1157 TIGR00594: DNA polymerase III, alpha subunit" amino acids 6 to 1029 (1024 residues), 1366.9 bits, see alignment E=0 PF02811: PHP" amino acids 8 to 172 (165 residues), 144.6 bits, see alignment E=1.1e-45 PF07733: DNA_pol3_alpha" amino acids 292 to 558 (267 residues), 353 bits, see alignment E=3.6e-109 PF17657: DNA_pol3_finger" amino acids 561 to 735 (175 residues), 213.5 bits, see alignment E=3.7e-67 PF14579: HHH_6" amino acids 808 to 896 (89 residues), 98.7 bits, see alignment 5.3e-32 PF01336: tRNA_anti-codon" amino acids 999 to 1068 (70 residues), 35.8 bits, see alignment 1.9e-12 PF20914: DNA_pol_IIIA_C" amino acids 1101 to 1149 (49 residues), 43.9 bits, see alignment (E = 5.2e-15)

Best Hits

Swiss-Prot: 73% identical to DPO3A_ECO57: DNA polymerase III subunit alpha (dnaE) from Escherichia coli O157:H7

KEGG orthology group: K02337, DNA polymerase III subunit alpha [EC: 2.7.7.7] (inferred from 75% identity to aha:AHA_1188)

MetaCyc: 73% identical to DNA polymerase III subunit alpha (Escherichia coli K-12 substr. MG1655)
DNA-directed DNA polymerase. [EC: 2.7.7.7]

Predicted SEED Role

"DNA polymerase III alpha subunit (EC 2.7.7.7)" in subsystem DNA-replication (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 A1S4Q5 at UniProt or InterPro

Protein Sequence (1157 amino acids)

>Sama_1154 DNA polymerase III subunit alpha (RefSeq) (Shewanella amazonensis SB2B)
MSQPRFVHLRVHSDFSMTDGLAKVKPILGKAEAEGMAAIALTDQNNLCGLVKFYSTCHDK
GIKPIIGADFWMLVPGFEDEFCAVTVLAMDNEGYQNLTQLISQAYLRGQVQGRVAIDQEW
LLTYNSGILLLSGAKEGDLGKALIKGNAAQAASLTQFYQKHFPDRYFIELIRTGRADEET
YLHMAVKHAAEVGLPVVATNQVVFLSPEDFEAHEIRVAIHDGFTLADNRRPKKYSEQQYL
RSEDEMCELFSDIPEAIENTVEIAKRCNVTVRLGEYFLPNFPTGELSTADFLVERSKEGL
EERLEFLFPDPAERAEKRKEYDERLDIELQVINQMGFPGYFLIVMEFIQWGKDNGIPVGP
GRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMDRRDEVIDHVAE
LYGREAVSQIITFGTMAAKAVVRDVGRVLGHSYGFVDRISKMIPPEPGMTLAKAFEVEPG
LQEAYDADEEVKDLIDMARKLEGVTRNAGKHAGGVVIAPTKITDFSPLYCDAEGKNPVTQ
FDKNDVEYAGLVKFDFLGLRTLTIIDWALGMINPRLAKLGKPPVDIAAIPLDDSKSFSVL
KRYETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGHEE
ISYPDATWQHESLKPILEPTYGIILYQEQVMQIAQTLAGYTLGGADMLRRAMGKKKPEEM
AKQRAGFEAGSVKNGVDGELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKTHFPS
EFMAAVMSADMDNTDKIVTLVDECDRMGLKIIPPDVNKGLFKFTVDEDLNIVYGIGAIKG
VGEGPVEAILEARKDGPFTDLFDFCARIDLKKLNKRVIEKLIYSGALDSLGPHRASMMAT
LPEAMQAADQHAKAQATGQHDMFGLLNDDQQDEKQQFVECTPWPDKIWLEGERETLGLYL
TGHPINQYLKELKNYTSGRLKDIHPTERGKTVKAAGLVVASRVMLTKRGSKMGLLTLDDK
SARLEVMLFTEAFEKFGHLLEKDRILICEGEVSFDDFSGGNRMTARNIIDISEARSHFAK
ALEVDLASQQATEAMLDKFFDVITPWKGGAVPLIVNFSRADASGRLQLGDDWRVDPSDDL
VLALQTLIGPDKIRIQF