Protein Info for PS417_13125 in Pseudomonas simiae WCS417

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 819 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 5 to 163 (159 residues), 230.1 bits, see alignment E=2e-72 PF13298: LigD_N" amino acids 39 to 144 (106 residues), 148.8 bits, see alignment E=1.5e-47 TIGR02779: DNA ligase D, ligase domain" amino acids 208 to 507 (300 residues), 348.8 bits, see alignment E=4.9e-108 PF01068: DNA_ligase_A_M" amino acids 208 to 388 (181 residues), 82.2 bits, see alignment E=1.1e-26 TIGR02776: DNA ligase D" amino acids 218 to 800 (583 residues), 744.4 bits, see alignment E=2.2e-227 PF04679: DNA_ligase_A_C" amino acids 407 to 501 (95 residues), 96.1 bits, see alignment E=3.3e-31 TIGR02778: DNA ligase D, polymerase domain" amino acids 527 to 771 (245 residues), 295.3 bits, see alignment E=7.9e-92 PF21686: LigD_Prim-Pol" amino acids 544 to 796 (253 residues), 300.5 bits, see alignment E=2.7e-93 PF01896: DNA_primase_S" amino acids 646 to 766 (121 residues), 27.2 bits, see alignment E=1.1e-09

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 72% identity to pmy:Pmen_3217)

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 A0A1N7UKV2 at UniProt or InterPro

Protein Sequence (819 amino acids)

>PS417_13125 ATP-dependent DNA ligase (Pseudomonas simiae WCS417)
MSKPLSEYNRKRDFGITAEPAGSAPAGKRKASALSFVIQKHDARNLHYDFRLELDGVLLS
WAVPKGPSLDPSHKRLAVHVEDHPLSYGGFEGSIPAGQYGAGDVIVWDRGIWQPHDEPRK
AYAAGKLKFTLVGEKLSGDWALVRTRLKGSGDKEQWLLIKEKDPQARSADDYDIVQAQPN
SVLSDASVGKPKTRAKARKTALPEQFTPQLATLVDRAPEGDWQYEIKFDGYRMLARIQAG
EVRLFTRNGHDWTECLPRQVKALQALKLKDSWLDGEVVSLNGDGLPDFQALQNAFDIGRS
LDIVYYLFDAPFLNGEDRRQAPVEERRAALKEALAGSRSTLLRYSEAFTAHHRDIFESAC
DLALEGVIGKRLGSPYVSRRSADWIKLKCRLSQEFVIVGYTRPQGSRSGFGALLLAVNND
TGLVYAGRVGTGFDQAALKAIYAQLTPLECETSPLAKPLSSAQARGVHWVKPTLVAQVQF
AEWTREDVVRQAAFVGLRTDKPVAQVVHEQPRTVHSKKPVKKTSRDVNITHPDRVIDKHS
GTQKQQLAQFYDTISQWILPFLRHRPVSLLRAPEGIEGEQFFQKHSERLAIPNIKQLDQS
LDPGHARLMEIDNVGALIGAVQMGSVEFHTWGATSDKIETPDLFVLDLDPDPALPWKAML
EAAQLTLSVLDELGLQAFVKTSGGKGLHLIVPLARRDNWETVKAFAKGIAQFMTEQLPER
FTATSGPKNRVGKIFIDYLRNARGASTVAAYSVRARPGLPVSVPVSREELEGLRGAQQWT
VANVLQRLNALKADPWAGYANRQKISKKMWDKLGAHPPE