Protein Info for Psyr_3245 in Pseudomonas syringae pv. syringae B728a ΔmexB

Annotation: ATP-dependent DNA ligase LigD phosphoesterase module / ATP-dependent DNA ligase LigD polymerase module

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 866 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 6 to 165 (160 residues), 231.3 bits, see alignment E=8.5e-73 PF13298: LigD_N" amino acids 41 to 146 (106 residues), 151.9 bits, see alignment E=1.5e-48 TIGR02779: DNA ligase D, ligase domain" amino acids 239 to 539 (301 residues), 373.9 bits, see alignment E=1.1e-115 PF01068: DNA_ligase_A_M" amino acids 243 to 419 (177 residues), 89 bits, see alignment E=8.6e-29 TIGR02776: DNA ligase D" amino acids 248 to 848 (601 residues), 787.3 bits, see alignment E=2.4e-240 PF04679: DNA_ligase_A_C" amino acids 438 to 533 (96 residues), 95.5 bits, see alignment E=5.2e-31 TIGR02778: DNA ligase D, polymerase domain" amino acids 577 to 819 (243 residues), 292 bits, see alignment E=8e-91 PF21686: LigD_Prim-Pol" amino acids 592 to 844 (253 residues), 301.9 bits, see alignment E=1e-93 PF01896: DNA_primase_S" amino acids 694 to 814 (121 residues), 38.8 bits, see alignment E=3.2e-13

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 100% identity to psb:Psyr_3245)

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 Q4ZRE5 at UniProt or InterPro

Protein Sequence (866 amino acids)

>Psyr_3245 ATP-dependent DNA ligase LigD phosphoesterase module / ATP-dependent DNA ligase LigD polymerase module (Pseudomonas syringae pv. syringae B728a ΔmexB)
MAKPASEYTRKRNFAITSEPAESKRKGKGKSQPGALGFVIQKHDARNLHYDFRLELDGTL
KSWAVPKGPSLDPTQKRLAVHVEDHPLDYAGFEGSIPQGQYGGGDVIVWDRGVWQPHGDP
QKTYEEGKLKFTLVGEKLSGDWALVRTRLKGSGSKEQWLLIKEKDDVARPAAEYDITHEQ
PQSVISGAHVGKQRGTSKKSGASAAKAKAATPAAAKASMPAAKPARRKAKSAFLDTLAPQ
LATLVEAPPAGDWLYEIKFDGYRMLTRIQGDDVRLFTRNGHDWTERLPELVKALKGMKLR
DSWFDGEVVVLDEQGLPDFQGLQNAFDAGNSKDILYYLFDMPFLSAEDLREVPLEQRRDA
LKQVLDAQKSRLLRYSDAFQAGHQDIVASAAAMGLEGVIGKRAGSAYVSKRNADWIKLKC
RLRQEFVVVGYTAPQGSRSAFGALLLAVNAGEDGLIYAGRVGTGFTEVSLEQLHKQLKKL
QRKDSPLAKKLSASQARGVQWVAPQLVCEAEFAQWTREGIVRQAAFVGLRSDKPAKDVVR
EDAQPAKVASQPPTTTAAPKARKKAAQGKVDVAGTGISHPDRVIDSKSGTSKIELAQFYQ
SIADWILPYLNKRPVALLRCPEGIDGEQFFQKHAEHLAIPHIRQLDRALDPGHAALMEID
SVPALVGAAQMGAIELHTWGATRDRIETPDHFVLDLDPDPALPWRSMIEATQMVLAVLEE
LGLEAFLKTSGGKGMHIIVPLARQADWDTVKAFAKAIAEFASRQLPERFTATMGPKNRVG
KIFIDYLRNSRGGSTVTAYSVRARPGLPVSVPIALDELAGLKSSAQWDITNLEQRLKRLK
DDPWAGYSNRRKITQRMWKQLGAKRP