Protein Info for Atu5055 in Agrobacterium fabrum C58

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 884 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 6 to 165 (160 residues), 238.9 bits, see alignment E=4e-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 254 to 550 (297 residues), 343 bits, see alignment E=3e-106 TIGR02776: DNA ligase D" amino acids 263 to 863 (601 residues), 732 bits, see alignment E=1.3e-223 PF01068: DNA_ligase_A_M" amino acids 266 to 434 (169 residues), 88.7 bits, see alignment E=9e-29 PF04679: DNA_ligase_A_C" amino acids 450 to 544 (95 residues), 95.6 bits, see alignment E=3.8e-31 TIGR02778: DNA ligase D, polymerase domain" amino acids 586 to 836 (251 residues), 306.2 bits, see alignment E=3.7e-95 PF21686: LigD_Prim-Pol" amino acids 606 to 856 (251 residues), 289 bits, see alignment E=7.4e-90

Best Hits

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

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

See Q7D410 at UniProt or InterPro

Protein Sequence (884 amino acids)

>Atu5055 ATP-dependent DNA ligase (Agrobacterium fabrum C58)
MASDKLSTYKQKRDFQKTQEPSGAAKLKASNRRRFVIQKHDATRLHYDLRLELDGVFKSW
AVTKGPSLDPHDKRLAVEVEDHPLDYGDFEGTIPKGQYGGGTVMLWDRGYWEPEGNKTPE
QALAKGDFKFTLEGERLHGSFVLVRMRNDRDGGKRTNWLLIKHRDDFSVEEKGAAVLDEN
DTSVASGRTMEAIAAGKGRKPKPFMVQSGDVQADAVWDSNHGLAAEERASDTKAKRKPAL
KKPAKSTMPEFIPPQLCETLDRPPSAKGWIHEIKFDGYRIQTRIENGEVTLKTRKGLDWT
AKYPAIATSAANLPDAIIDGEICALDENGAPDFAALQAALSEGKTDELVYFAFDLLFEEN
EDLRQLPLTERKERLQTLLDDAGEDPRLRFVEHFETGGDAVLKSACKLSLEGIVSKQADA
PYQSGRTETWAKSKCRAGHEVVIGAYAKTNGKFRSLLVGVFKGDHFVYVGRVGTGYGAKT
VDTILPRLRELETSKSPFTGIGAPKKDPNVVWVKPELVAEIQFAGWTADGLVRQAAFKGL
REDKPAHEVEAEKPASPAKTDTPTPAKSKPSRPARGKNAKAEVMGVMISSPDKALWPDAN
DGEPVTKEDLARYHEAVGPWLIDHIKGRPCSIIRTPDGIGGEVFFQRHAMPGTSNLIELV
KVFGDKKPYLQIDRVEGLAAIAQIGGVELHPWNCEPGQPEVPGRLVFDLDPGPDVPFSTV
VEAAREMRDRLEELGLVSFCKTTGGKGLHVVTPLAVPKGKKLSWPEAKGFAHDVCMQMAR
ETPELYLIKMAKNQRNGRIFLDYLRNDRMATAVAPLSPRARAGAPVSMPLSWKQVKTDLD
PKRFTIRTVPALLSKTTAWQDYCDGQRSLEQAIKRLAKSMKQAA