Protein Info for BPHYT_RS09215 in Burkholderia phytofirmans PsJN

Annotation: ATP-dependent DNA 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 940 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 6 to 175 (170 residues), 213 bits, see alignment E=3.7e-67 PF13298: LigD_N" amino acids 48 to 156 (109 residues), 151.7 bits, see alignment E=1.8e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 282 to 587 (306 residues), 338.9 bits, see alignment E=5.3e-105 TIGR02776: DNA ligase D" amino acids 292 to 923 (632 residues), 717.6 bits, see alignment E=3.1e-219 PF01068: DNA_ligase_A_M" amino acids 294 to 467 (174 residues), 85.7 bits, see alignment E=9.3e-28 PF04679: DNA_ligase_A_C" amino acids 486 to 581 (96 residues), 94.1 bits, see alignment E=1.4e-30 TIGR02778: DNA ligase D, polymerase domain" amino acids 650 to 893 (244 residues), 299.4 bits, see alignment E=4.5e-93 PF21686: LigD_Prim-Pol" amino acids 667 to 918 (252 residues), 317.6 bits, see alignment E=1.7e-98 PF01896: DNA_primase_S" amino acids 768 to 889 (122 residues), 31 bits, see alignment E=7.7e-11

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 100% identity to bpy:Bphyt_1858)

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)

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 B2T3V5 at UniProt or InterPro

Protein Sequence (940 amino acids)

>BPHYT_RS09215 ATP-dependent DNA ligase (Burkholderia phytofirmans PsJN)
MNDRLDLYNRKRRFDDTPEPAGTRARRKPAGRKTTRQAAGEALSYVIQEHDARRLHYDFR
LELNGTLLSWAVPKGPSLDPSVKRLAVHVEDHPVEYGSFEGEIPPGNYGAGSVIVWDRGT
WEPVGGAAEAARSYAAGKLKFHLHGEKLHGGWTLVRSHMRGSGDKEQWLLIKERDDEARD
ESDYDILKKRPGSVLSGSASVAKGEKTTTAASKTARKTAASDAKSTAKRGGKSSAKAASS
TRADPRRPDIVATRNTQSLRELAATPSIEGAVKARLPTTFKPQLATLVDAAPPGDEWSYE
IKFDGYRVLARIDRDAKGSAVKVFTRAGNDWTAKFSKQVKAFEQLGIESAWLDGEAVVLD
PNGVPNFQALQNAFDANRPQDIIVYLFDIPFLNGYDLRGVPLEQRRAILHALMEDVDDSV
LRFSNNFDFSAEDLLRSACDMALEGIIGKRRDSGYLSGRSSTWIKLKCRRRQEFVIGGYS
EPSGSRAAFGALLLGVYDSKGNLNYAGRVGTGFDAALLRSVKKELDAHATKRMPFAAVPR
ERSRTPVHWVEPVLVAECNFAEWTSDGIVRQASFVSLRNDKPARQIVKETPRQGADVQQQ
TDSISDDAPKKRAARKTSGSNVAAAGKTTAAKPKTAKSPTTAPPAEVAGVRISHPDRVID
KSSGARKIDLVQYYESVAEWMLPHLKDRPVSLVRAPEDIGGELFFQKHSQKLSIPNVTQH
PGLDPGHPPLITVDTIKALVGAAQMGTVEFHTWNAVASNIEKPDRAVFDLDPDAALGWER
MIEAAQLTRSLLEELGLTSFCKTSGGKGLHVVVPLAKQAGWDEVKDFSQAVAQHMAATLP
KYFSAKMGAQNRKQKIFVDYLRNNRGSSTVAAFSARARPGLGVSVPLAWDEVAGTTGGDQ
WTIENLHERLAELKSDPWADYAKTRQRITAAMKKRLNDAQ