Protein Info for MMJJ_RS03300 in Methanococcus maripaludis JJ

Annotation: RNA ligase

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 50 100 150 200 250 300 350 394 TIGR01209: RNA ligase, Pab1020 family" amino acids 22 to 394 (373 residues), 433.9 bits, see alignment E=2.2e-134 PF01068: DNA_ligase_A_M" amino acids 88 to 249 (162 residues), 39 bits, see alignment E=1.1e-13 PF09414: RNA_ligase" amino acids 98 to 256 (159 residues), 102.3 bits, see alignment E=5.4e-33 PF18330: Lig_C" amino acids 267 to 392 (126 residues), 149.1 bits, see alignment E=9.8e-48

Best Hits

Swiss-Prot: 53% identical to Y414_METJA: Uncharacterized protein MJ0414 (MJ0414) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

KEGG orthology group: K07468, putative ATP-dependent DNA ligase [EC: 6.5.1.1] (inferred from 96% identity to mmp:MMP0376)

Predicted SEED Role

"ATP-dependent DNA ligase, homolog of eukaryotic ligase III"

Isozymes

Compare fitness of predicted isozymes for: 6.5.1.1

Use Curated BLAST to search for 6.5.1.1

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

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

Search structures

Predict protein localization: PSORTb (archaea)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (394 amino acids)

>MMJJ_RS03300 RNA ligase (Methanococcus maripaludis JJ)
MDKTYFSEDILNFEEFIIDASKKLNIDEDSLKSGFKRKLITKYEYNGEKYLCFKKKLKHI
ERGTILFLNDNLDFIIGYPKIRRAMVLESSVKKYFNGKIAVEEKLDGYNIRIVKMHDEII
AITRGGKICPFTTKKVKKYINTKFLDDFPELMLCGEMVGLNNPYVNHYYPEADKTYENLG
FYIFDVRNKETNLALSIYEKEKILDEYNIPYVKPIKIIDSRDIDELWDILDDLNENHREG
VVLKDPEMIKNPIKYTTHSTQCGDLSIAFSYVYDLGIDFMFSRLVREGYQSFEKCESEEE
RKKRAHDLGESILLPMVETINEISKESVAKECFELYFDSEAEFNEFINYLKTMHINFTVE
SREYIKKDIFKAKINRIYNSTSDKIKSHLDGNLW