Protein Info for ABIE40_RS29525 in Rhizobium sp. OAE497

Annotation: DNA ligase D

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 887 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 6 to 165 (160 residues), 237.8 bits, see alignment E=8.5e-75 PF13298: LigD_N" amino acids 38 to 145 (108 residues), 152.4 bits, see alignment E=8.4e-49 TIGR02779: DNA ligase D, ligase domain" amino acids 257 to 553 (297 residues), 329.3 bits, see alignment E=4.3e-102 TIGR02776: DNA ligase D" amino acids 266 to 866 (601 residues), 713.1 bits, see alignment E=7.1e-218 PF01068: DNA_ligase_A_M" amino acids 269 to 437 (169 residues), 87.2 bits, see alignment E=2.5e-28 PF04679: DNA_ligase_A_C" amino acids 453 to 547 (95 residues), 92.2 bits, see alignment E=4.4e-30 TIGR02778: DNA ligase D, polymerase domain" amino acids 589 to 839 (251 residues), 303.5 bits, see alignment E=2.5e-94 PF21686: LigD_Prim-Pol" amino acids 609 to 858 (250 residues), 291.6 bits, see alignment E=1.1e-90

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 91% identity to atu:Atu5055)

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

Find the best match in UniProt

Protein Sequence (887 amino acids)

>ABIE40_RS29525 DNA ligase D (Rhizobium sp. OAE497)
MASDKLSTYKQKRDFQKTQEPSGAAKLKASTRRRFVIQKHDATRLHYDLRLELDGVFKSW
AVTKGPSLDPHDKRLAVEVEDHPLDYGDFEGTIPKGQYGGGTVMLWDRGYWEPEGNKTPE
QALAKGDFKFTLEGERLHGSFVLVRMRSDRDGGKRTNWLLIKHHDDFSVEEDGAAVLEDN
ATSVASGRTMEAIAAGKGRKPKPFMVQSGDVQADAVWDSNHGLAAEGRKAETKTKRTSAA
AKSAKPAKSVMPEFIPPQLCETLERPPSAGGWVHEIKFDGYRIQARIENGEVTLKTRKGL
DWTAKYPAIATSAANLPDAIIDGEICALDENGAPDFAALQAALSEGKTDALVYFAFDLLF
EGDEDLRQLPLIKRKERLQRLLDGAGEDSRLRFVEHFETGGDAVLKSACKLSLEGIVSKQ
ADGLYESGRTKTWAKSKCRAGHEVVIGAYAKTNGKFRSLLVGVFRGYHFVYVGRVGTGYG
AKTVDAILPKLRKIETDKSPFTGIGAPKKDPNIVWVEPELVAEIQFAGWTADGLVRQAAF
KGLREDKPAAEVEAEMPASPAKTETPAPAATKPSRPARGKNAKAEVMGVMISSPDKALWP
DANDGVPVTKENLAHYYEAVGPWLIDHIKGRPCSIIRTPDGIGAEQFFQRHAMPGTSNLL
ELVKVFGDKKPYLQIDRVEGLAAIAQIGGVELHPWNCEPGQPEVPGRLVFDLDPGPDVPF
STVVEAAREMRDRLEELGLVSFCKTTGGKGLHVVTPLAVAKGKKLTWPEAKAFAHDVCLQ
MARDNPDIYLIKMAKNQRNGRIFLDYLRNDRMATAVAPLSPRARPGATVSMPLTWSQVKT
DLDPKRFTIRTVPALLSKTIAWQDYCDGQRSLEQAIKRLGKMMNVAA