Protein Info for ABZR87_RS08115 in Ralstonia sp. UNC404CL21Col

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 867 TIGR02777: DNA ligase D, 3'-phosphoesterase domain" amino acids 5 to 167 (163 residues), 237.9 bits, see alignment E=8.1e-75 PF13298: LigD_N" amino acids 41 to 146 (106 residues), 157.2 bits, see alignment E=3.6e-50 TIGR02779: DNA ligase D, ligase domain" amino acids 234 to 539 (306 residues), 353.1 bits, see alignment E=2.5e-109 TIGR02776: DNA ligase D" amino acids 243 to 849 (607 residues), 738.7 bits, see alignment E=1.2e-225 PF01068: DNA_ligase_A_M" amino acids 247 to 419 (173 residues), 96 bits, see alignment E=6.5e-31 PF04679: DNA_ligase_A_C" amino acids 438 to 533 (96 residues), 103 bits, see alignment E=2.4e-33 TIGR02778: DNA ligase D, polymerase domain" amino acids 574 to 820 (247 residues), 299.8 bits, see alignment E=3.4e-93 PF21686: LigD_Prim-Pol" amino acids 590 to 845 (256 residues), 316.3 bits, see alignment E=4.1e-98 PF01896: DNA_primase_S" amino acids 693 to 815 (123 residues), 28.5 bits, see alignment E=4.8e-10

Best Hits

KEGG orthology group: K01971, DNA ligase (ATP) [EC: 6.5.1.1] (inferred from 96% identity to rpf:Rpic12D_0488)

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 (867 amino acids)

>ABZR87_RS08115 DNA ligase D (Ralstonia sp. UNC404CL21Col)
MPRHLADYRRKRDFTQTQEPAGARRKADERRDNDALHFVIQKHDATRLHYDFRLELDGTL
KSWAVPKGPSLDPADKRLAVHVEDHPLDYADFEGHIPEGQYGGGDVIVWDRGTWHPHGDP
RKAYRDGKLKFDLDGEKLHGAWALVRTHLHGTGRHPKEQWLLIKERDDQVRPSSDYDVTQ
ALPASVITGENVGAKPKAKGRAKADGGKAEHSKPAQVQPPAGAVPATLPRTLEPQLATLV
DGPPTQGEWDYEVKFDGYRILARIDGNTVRLFSRNGRDWTAKLPRQARTLPALGLREAWL
DGEVVVMGERGVPDFQALQNAFETAHAEHIAYYLFDIPFCNGMDLRGVPLRERRALLQRI
FEAAPGDLDRDAVLFSGTFNAAPEDLLSSACSMSLEGVIGKRADAPYRAGRSPAWIKLKC
GQRQEFVIGGYSAPKGSRSGFGALLLGVYDDAGKLRYAGRVGTGFNETSLHALHHELTGL
TIDTPPFANPPTGSDARDVQWVKPERVAEIAFAEWTREGIVRQAVFQGLRDDKPARNIVR
EQAKPPSAAARKETRAVNAAERKVRPGAERIADVDVTHPDRVIEKASGTTKADLARYYAS
VAEWMLPHLHNRPTSLVRAPDGIDGERFFQKHSAALKLQGITQLDPSLDPGHPSLLAINS
AEALVGAVQMGTVEFHTWNALADRIEQPDRIVFDIDPDPALPFARVIEATQLMLAMLDEL
GLKAFLKTSGGHGMHVVVPLTRREASGWDTLKTFAQAVVQHMAATFPDRFVAKMGPQNRV
GKIFIDYLRNNRGASTVAAYSVRARTGLPVSVPIRHDELEGLQSSAQWTLRTLPDRLAKL
KGDPWADYAGTRQSVTADMRKRIGAND