Protein Info for Rv0938 in Mycobacterium tuberculosis H37Rv

Annotation: ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 759 TIGR02778: DNA ligase D, polymerase domain" amino acids 9 to 261 (253 residues), 305.3 bits, see alignment E=7.3e-95 PF21686: LigD_Prim-Pol" amino acids 25 to 283 (259 residues), 281.6 bits, see alignment E=1.6e-87 PF01896: DNA_primase_S" amino acids 136 to 257 (122 residues), 34.2 bits, see alignment E=8.1e-12 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 297 to 446 (150 residues), 204.8 bits, see alignment E=1.3e-64 PF13298: LigD_N" amino acids 329 to 433 (105 residues), 137.8 bits, see alignment E=3.7e-44 TIGR02779: DNA ligase D, ligase domain" amino acids 460 to 757 (298 residues), 325.9 bits, see alignment E=4.7e-101 PF01068: DNA_ligase_A_M" amino acids 461 to 637 (177 residues), 100.2 bits, see alignment E=3.2e-32 PF04679: DNA_ligase_A_C" amino acids 657 to 751 (95 residues), 91.5 bits, see alignment E=9.1e-30

Best Hits

Swiss-Prot: 100% identical to LIGD_MYCTU: Multifunctional non-homologous end joining DNA repair protein LigD (ligD) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 100% identity to mtu:Rv0938)

Predicted SEED Role

"ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD" in subsystem DNA Repair Base Excision (EC 6.5.1.1)

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)

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

Find the best match in UniProt

Protein Sequence (759 amino acids)

>Rv0938 ATP dependent DNA ligase LigD (ATP dependent polydeoxyribonucleotide synthase) (thermostable DNA ligase) (ATP dependent polynucleotide ligase) (sealase) (DNA repair enzyme) (DNA joinase) (Mycobacterium tuberculosis H37Rv)
MGSASEQRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQ
PAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAE
PGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLY
TPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAP
YSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDADAPVADRLTRY
RRMRDASKTPEPIPTAKPVTGDGNTFVIQEHHARRPHYDFRLECDGVLVSWAVPKNLPDN
TSVNHLAIHTEDHPLEYATFEGAIPSGEYGAGKVIIWDSGTYDTEKFHDDPHTGEVIVNL
HGGRISGRYALIRTNGDRWLAHRLKNQKDQKVFEFDNLAPMLATHGTVAGLKASQWAFEG
KWDGYRLLVEADHGAVRLRSRSGRDVTAEYPQLRALAEDLADHHVVLDGEAVVLDSSGVP
SFSQMQNRGRDTRVEFWAFDLLYLDGRALLGTRYQDRRKLLETLANATSLTVPELLPGDG
AQAFACSRKHGWEGVIAKRRDSRYQPGRRCASWVKDKHWNTQEVVIGGWRAGEGGRSSGV
GSLLMGIPGPGGLQFAGRVGTGLSERELANLKEMLAPLHTDESPFDVPLPARDAKGITYV
KPALVAEVRYSEWTPEGRLRQSSWRGLRPDKKPSEVVRE