Protein Info for DDA3937_RS17095 in Dickeya dadantii 3937

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 50 100 150 200 250 300 350 400 450 500 550 600 650 683 PF01653: DNA_ligase_aden" amino acids 15 to 329 (315 residues), 455.4 bits, see alignment E=3.7e-140 TIGR00575: DNA ligase, NAD-dependent" amino acids 22 to 678 (657 residues), 887.2 bits, see alignment E=3.3e-271 PF03120: DNA_ligase_OB" amino acids 333 to 409 (77 residues), 119.1 bits, see alignment E=2.2e-38 PF03119: DNA_ligase_ZBD" amino acids 418 to 445 (28 residues), 41.8 bits, see alignment (E = 2.7e-14) PF14520: HHH_5" amino acids 458 to 513 (56 residues), 27.6 bits, see alignment 1.1e-09 amino acids 522 to 565 (44 residues), 29.4 bits, see alignment 3.3e-10 PF12826: HHH_2" amino acids 521 to 584 (64 residues), 79.8 bits, see alignment E=4.8e-26 PF00533: BRCT" amino acids 608 to 681 (74 residues), 59.6 bits, see alignment E=1e-19 PF12738: PTCB-BRCT" amino acids 626 to 673 (48 residues), 25.4 bits, see alignment 4.1e-09

Best Hits

Swiss-Prot: 82% identical to DNLJ_PECAS: DNA ligase (ligA) from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)

KEGG orthology group: K01972, DNA ligase (NAD+) [EC: 6.5.1.2] (inferred from 100% identity to ddd:Dda3937_00179)

MetaCyc: 77% identical to DNA ligase (Escherichia coli K-12 substr. MG1655)
DNA ligase (NAD(+)). [EC: 6.5.1.2, 6.5.1.6]

Predicted SEED Role

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

MetaCyc Pathways

Isozymes

Compare fitness of predicted isozymes for: 6.5.1.2

Use Curated BLAST to search for 6.5.1.2 or 6.5.1.6

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

See E0SDN5 at UniProt or InterPro

Protein Sequence (683 amino acids)

>DDA3937_RS17095 NAD-dependent DNA ligase LigA (Dickeya dadantii 3937)
MLEKESKPADDISTVSVQIEALRAQLRYHEYKYHVEDAPEIPDAEYDKLMNALKTLEQAH
PELVTPDSPTQRVGATPLDAFDTIAHEVPMLSLDNVFDETSFLAFSKRINDRLKNDGELT
FCCELKLDGLAVSLLYENGLLVRAATRGDGTTGENITANIRTVGAIPLRLRGDNIPQRLE
VRGEVFMKHKGFEALNEEARRTGGKVFANPRNAAAGSLRQLDPRITATRPLTFLCYGVGL
VEGGALPDTHWQRLMQFRDWGLPVSDRIRLCTGSDAVLDFYRQVEQERETLGFDIDGVVI
KVNELTLQERLGFVARAPRWAVAFKFPAQEQLTWLRDVEFQVGRTGAITPVARLEPVAVA
GVVVSNATLHNADEIERLGIQIGDRVAVRRAGDVIPQIVSVVLSERPADARPVVFPEQCP
VCGSELERVDGEAVTRCTGGLFCGAQRKEALKHFVSRRALDVEGMGDKIIDQLVEKEYVK
TPADLFRLSAGILTGLDRMGPKSAQNLVNALNKAKSTTFARFLYALGIRDVGEATAASLA
SHFGTLEALQSADLEALQQVQDVGIVVATHVRNFLDEAHNQQVIQELISENIGIHWPAPV
VVDVEASDSPFAGKTVVLTGSLTLLSRDEAKDRLTALGAKVSGSVSKKTDLVIAGEAAGS
KLTKAQELGIEVIDEAEMMRLLG