Protein Info for GFF111 in Hydrogenophaga sp. GW460-11-11-14-LB1

Annotation: ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 834 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 10 to 164 (155 residues), 222.1 bits, see alignment E=6e-70 PF13298: LigD_N" amino acids 41 to 146 (106 residues), 143.4 bits, see alignment E=6.7e-46 TIGR02779: DNA ligase D, ligase domain" amino acids 211 to 510 (300 residues), 331 bits, see alignment E=1.3e-102 PF01068: DNA_ligase_A_M" amino acids 223 to 393 (171 residues), 81.4 bits, see alignment E=1.9e-26 TIGR02776: DNA ligase D" amino acids 225 to 817 (593 residues), 654.7 bits, see alignment E=3.4e-200 PF04679: DNA_ligase_A_C" amino acids 412 to 504 (93 residues), 97.1 bits, see alignment E=1.6e-31 TIGR02778: DNA ligase D, polymerase domain" amino acids 545 to 789 (245 residues), 283.4 bits, see alignment E=3.5e-88 PF21686: LigD_Prim-Pol" amino acids 560 to 813 (254 residues), 285.7 bits, see alignment E=9.3e-89 PF01896: DNA_primase_S" amino acids 664 to 785 (122 residues), 31.3 bits, see alignment E=6.3e-11

Best Hits

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 (834 amino acids)

>GFF111 ATP-dependent DNA ligase (EC 6.5.1.1) clustered with Ku protein, LigD (Hydrogenophaga sp. GW460-11-11-14-LB1)
MTGPPSSDLLQPYKAKRDFARTPEPPGELGRAAKVLGFVVQKHWAGRLHYDFRIELDGVM
KSWAVPKGPSLDPGDKRMAVEVEDHPLAYASFEGTIPPRQYGAGKVIVWDKGVWAPEGDP
HAGLRSGNLKFELLGHKLRGRWALVRMKTRDEKKPAWLLIKERDAFARSAEEFSVVDAAP
DSVASQRMPSKDAGAWPPEAVPSALPATLSPQLATRSEAAPAVDADWLYEIKFDGYRMLA
RVDGADVKLFTRNGHDWTHRLRPLHKALQDMQLPPGWYDGEIVVFGGTGLPDFGALQQSL
ENERTASVVFYLFDLPYVAGHDLRAAPLVARRAVLEGLLRERPMDAVRFSAVFEASAASV
LMSACRLGLEGVIAKRKSAPYRSTRSADWLKLKCGQRQAFVIGGFTEGKGSRTGFGSLLL
GLHEADGSLRHVGNVGTGFDTGTLSSLHRKLKALERRTSPFAQATIAGRPHWATPSLVAE
VAFSDWTHAGHIRHAVFVGLREDKAAPAVEKEVEVPKPNDSPAPVRKPGHPPVPAQKPPA
PSRMRVTHPERVIDASTGVTKLDLVSFYATVGPLMIEHLRQRPAALMRAPSGIEGELFFQ
KHLPPSMKMAGVVQLDPALDPGHDPWVAVASRRGLLSAAQWNVVEFHTQNAFARTFEKPN
RLVFDLDPGEGVAWAQVQEAAQLTHSLLDHLGLASFLKTSGGKGLHVVVPVRQQHDWDSV
KGFARALVRHMSETIPQRFVAKSGPRNRVGRIFVDYLRNGRGATTVSAWSARARPGMGVS
VPVDWSELSALRGGDHWHVRNIAERLSVGNRPWNGYARSARSLTPAMKMLGYAP