Protein Info for DZA65_RS06560 in Dickeya dianthicola ME23

Annotation: peptidoglycan DD-transpeptidase MrdA

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 50 100 150 200 250 300 350 400 450 500 550 600 636 transmembrane" amino acids 21 to 42 (22 residues), see Phobius details TIGR03423: penicillin-binding protein 2" amino acids 20 to 615 (596 residues), 786.8 bits, see alignment E=7e-241 PF03717: PBP_dimer" amino acids 65 to 240 (176 residues), 162.3 bits, see alignment E=1.8e-51 PF00905: Transpeptidase" amino acids 273 to 611 (339 residues), 269.2 bits, see alignment E=4.3e-84

Best Hits

Swiss-Prot: 81% identical to MRDA_ECOLI: Peptidoglycan D,D-transpeptidase MrdA (mrdA) from Escherichia coli (strain K12)

KEGG orthology group: K05515, penicillin-binding protein 2 (inferred from 98% identity to ddd:Dda3937_02483)

MetaCyc: 81% identical to peptidoglycan DD-transpeptidase MrdA (Escherichia coli K-12 substr. MG1655)
Serine-type D-Ala-D-Ala carboxypeptidase. [EC: 3.4.16.4]

Predicted SEED Role

"Penicillin-binding protein 2 (PBP-2)" in subsystem Peptidoglycan Biosynthesis

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

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 A0A385XUT9 at UniProt or InterPro

Protein Sequence (636 amino acids)

>DZA65_RS06560 peptidoglycan DD-transpeptidase MrdA (Dickeya dianthicola ME23)
MNIERKPFRDYTAEAALFVRRALVAFLGILLLSGILVANLYHLQVLRFDDYRTRSNENRI
KLVPIAPSRGIIYDRNGTPLALNRTIYQLELIPEKVNNLEETLQALKSIIDLTDEDIDNF
RKERKRSRRFTSIPVKTGLNEVQVASFAVNQYRFPGVEVKGYQRRYYPYGAALTHVIGYV
SKINDKDLERLDQEGELADYAATHDIGKLGIERYYEDVLHGKPGYEEVEVNNRGRVIRQL
HEQPPQAGKDITLTLDLNLQLYIEKLLAGSRAAVVVTDPKDASILAMVSTPSYDPNLFVD
GISSKTYHALLNDPNRPLINRATQGVYPPASTVKPYIAVSALSAGVITPYTSLFDPGWWQ
LPGSEKRFRDWKKWGHGRLNLTKSLEESADTFFYQVSYDMGIDRLSEWMSKFGYGHRTGI
DLSDKEESPGIMPTREWKMKRYKKPWYQGDTIPVGIGQGYWTATPIQMLKALTTLINDGQ
VKAPHLLSSTQENNTQVPYRQSEHQQIGDIRSGYWEIVKDGMYGVANRQNGTAHKFFADS
SYKIAAKSGTAQVFGLKENETYNANRIAERLRDHKLMVAFAPYSNPKVAMSIILENGGAG
PAVGTIVRQILDHIMLGDNNTSLPDAPPSPPGSETE