Protein Info for HMPREF1078_RS01725 in Parabacteroides merdae CL09T00C40

Annotation: NAD-dependent DNA ligase LigA

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 50 100 150 200 250 300 350 400 450 500 550 600 666 PF01653: DNA_ligase_aden" amino acids 3 to 313 (311 residues), 394.1 bits, see alignment E=1.4e-121 TIGR00575: DNA ligase, NAD-dependent" amino acids 10 to 660 (651 residues), 794 bits, see alignment E=5.6e-243 PF03120: DNA_ligase_OB" amino acids 317 to 390 (74 residues), 110.6 bits, see alignment E=8.2e-36 PF03119: DNA_ligase_ZBD" amino acids 404 to 429 (26 residues), 41.8 bits, see alignment (E = 2.4e-14) PF12826: HHH_2" amino acids 505 to 568 (64 residues), 89.5 bits, see alignment E=3.7e-29 PF14520: HHH_5" amino acids 510 to 557 (48 residues), 28 bits, see alignment 7.4e-10 PF00533: BRCT" amino acids 588 to 664 (77 residues), 59.1 bits, see alignment E=1.2e-19

Best Hits

Swiss-Prot: 86% identical to DNLJ_PARD8: DNA ligase (ligA) from Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)

KEGG orthology group: K01972, DNA ligase (NAD+) [EC: 6.5.1.2] (inferred from 86% identity to pdi:BDI_0799)

Predicted SEED Role

"DNA ligase (EC 6.5.1.2)" in subsystem DNA Repair Base Excision (EC 6.5.1.2)

MetaCyc Pathways

Isozymes

No predicted isozymes

Use Curated BLAST to search for 6.5.1.2

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 (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 (666 amino acids)

>HMPREF1078_RS01725 NAD-dependent DNA ligase LigA (Parabacteroides merdae CL09T00C40)
MVVKDKIKALREALEQHNYNYYVLSAPTISDREFDEMMKELQVLEESHPEYADPHSPTQR
VGSDLSKEFEQVVHKYPMLSLGNTYSEDEVKDFYERIARDLNEPFEIVAELKYDGTSISL
TYEDGRLVRAVTRGDGTRGDDVTANVKTIRSVPLKLMGDRYPATFEIRGEILLPWAEFDR
LNKEREEQEEPLFANPRNAASGTLKQQNPAVVAARKLDAYFYYLLGEELPAETHFDNLEA
ARSWGFKIPNVIRVCNSLEDIYGYIAYWDVERKNLPVATDGIVLKVNSLRQQRNLGFTAK
SPRWAIAYKFQAERAVTRLNSVSFQVGRTGAVTPVANLEPVLLAGTTVKRASLHNADIIE
GLDLHLGDKVFVEKGGEIIPKIVGVDVEARGLLVGDKVRFIRSCPECGTPLMRPEGEAAH
YCPNEAGCPPQIKGKIEHFVTRRAMNINMGPETVEDLYEAGYIKDTADLYTLEIADLLRL
ERWADKSARNLMASLEESKQVPFERVLYGLGIRFVGETVAKRLVSAFHSMEQLEQASFED
LTAVDEIGERIARSIIAYFADERNRTLVNRLKEYGLQMSVPEEKLANRSEKLKGLSIVIS
GTFAKHSRDEYKAMIEQHGGKNSGSVSGKTDYILAGDNMGPAKLEKAAKLGVKIINEDEF
LNMIAE