Protein Info for Rru_A1704 in Rhodospirillum rubrum S1H

Annotation: Serine-type D-Ala-D-Ala carboxypeptidase (NCBI)

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 50 100 150 200 250 300 350 388 signal peptide" amino acids 1 to 26 (26 residues), see Phobius details PF00768: Peptidase_S11" amino acids 23 to 250 (228 residues), 243.7 bits, see alignment E=3e-76 PF13354: Beta-lactamase2" amino acids 34 to 187 (154 residues), 55.5 bits, see alignment E=7.6e-19 PF07943: PBP5_C" amino acids 274 to 364 (91 residues), 62.3 bits, see alignment E=6.2e-21

Best Hits

Swiss-Prot: 41% identical to DACD_SALTY: D-alanyl-D-alanine carboxypeptidase DacD (dacD) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: K07258, D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5/6) [EC: 3.4.16.4] (inferred from 100% identity to rru:Rru_A1704)

MetaCyc: 40% identical to D-alanyl-D-alanine carboxypeptidase DacC (Escherichia coli K-12 substr. MG1655)
Serine-type D-Ala-D-Ala carboxypeptidase. [EC: 3.4.16.4, 3.4.17.8]; 3.4.16.4 [EC: 3.4.16.4, 3.4.17.8]; 3.4.16.4 [EC: 3.4.16.4, 3.4.17.8]; 3.4.16.4 [EC: 3.4.16.4, 3.4.17.8]

Predicted SEED Role

"D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4)" in subsystem Peptidoglycan Biosynthesis (EC 3.4.16.4)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 3.4.16.4

Use Curated BLAST to search for 3.4.16.4 or 3.4.17.8

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 Q2RTP1 at UniProt or InterPro

Protein Sequence (388 amino acids)

>Rru_A1704 Serine-type D-Ala-D-Ala carboxypeptidase (NCBI) (Rhodospirillum rubrum S1H)
MIALARHLTPFVLAAGLLTAMPAQAFETKARHALVIDLDTDTVLLDKDADVPMPPSSMSK
LMTAYMLFERLKSGSLSLDDTFSVSENAWRKGGAASGGSTMFLNPGAQVKVHDLMRGIII
QSGNDACVVVAENLAGDEATFAAAMNRRAKELGLTNSHFVNATGLPDPEHYMTAHDLVLL
AEHIIRDFPEFYEIYGETKFTYNGIVQHNRNPLLYMNMGADGLKTGHTNIAGFGLTASAV
QDGRRLLMVINGLQSNKERSEEAERLMSWGFRNFETVTLLKAGQPISDADVWMGEEETVP
LVSVNDLKITLPRAARRDMVAKAVFETPIPAPIQAGDRIATLVLTGPDMAKLEYPLVAGR
AVEQLSFFGRILASARNAVFGTAQPAAH