Protein Info for DDA3937_RS00195 in Dickeya dadantii 3937

Annotation: NAD-dependent DNA ligase LigB

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 50 100 150 200 250 300 350 400 450 500 560 signal peptide" amino acids 1 to 21 (21 residues), see Phobius details PF01653: DNA_ligase_aden" amino acids 31 to 308 (278 residues), 97.3 bits, see alignment E=1.5e-31 PF03120: DNA_ligase_OB" amino acids 314 to 385 (72 residues), 70.9 bits, see alignment E=1e-23

Best Hits

Swiss-Prot: 56% identical to LIGB_PECAS: DNA ligase B (ligB) 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_01130)

MetaCyc: 48% identical to DNA ligase B (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), LigB" (EC 6.5.1.2)

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 E0SEK5 at UniProt or InterPro

Protein Sequence (560 amino acids)

>DDA3937_RS00195 NAD-dependent DNA ligase LigB (Dickeya dadantii 3937)
MRYRYALAAVLFAVSGLAEAASCPAWSSTRAEQEITQLGQQLTQWDNAYYEQGQSPVDDQ
VYDQLRQTLATWQVCFQADAGRFAISLPTTGRRQHPVAHTGLKKLSEPTELKQWIAQHND
LWVQPKIDGVAVTLVYEQGKLVAAISRGNGRQGEDWTDKVRQMNSVPQQLSAMSGRQVFQ
GELYLQVTDHRQQQVGGINARAQVAGEMRRKQPSPLLSRIGVFVWAWPDGPADMPARLAK
LRELGFGLTADYTQPVSSLEAAAQWRERWYRAPLPFVTDGVVVRQAQEPAGRYWQDTPAE
WAVAWKYPLVNRVTEVTGVDVEVGRTGRMTVVLQLQPVILDDKTVSRVNLGSVSRWRQWD
VLPGDRVSISLAGLGIPRLDAVVWRGAVREAITVPATSPFDVFSCLQWSRECQPQFLARL
VWMSGRNGLSLSGISEATWQRLTQRGALVDVVSWLALEPAQLAAAGDFGEQQAERIHRQF
QLARRQPLRNWLLALGLPVPSRVRHALDGASLEQLQQRSAAEWQQFSGIGVRRAQRIRDF
LHHTDIVRQLAWLNEHGVKS