Protein Info for SO1168 in Shewanella oneidensis MR-1

Name: mrdA
Annotation: penicillin-binding protein 2 (NCBI ptt file)

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 50 100 150 200 250 300 350 400 450 500 550 618 transmembrane" amino acids 23 to 43 (21 residues), see Phobius details TIGR03423: penicillin-binding protein 2" amino acids 21 to 610 (590 residues), 777.7 bits, see alignment E=4e-238 PF03717: PBP_dimer" amino acids 66 to 241 (176 residues), 152.5 bits, see alignment E=1.7e-48 PF00905: Transpeptidase" amino acids 273 to 605 (333 residues), 237.2 bits, see alignment E=2.5e-74

Best Hits

Swiss-Prot: 50% identical to MRDA_ECOL6: Peptidoglycan D,D-transpeptidase MrdA (mrdA) from Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

KEGG orthology group: K05515, penicillin-binding protein 2 (inferred from 100% identity to son:SO_1168)

MetaCyc: 50% 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)

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 Q8EHP9 at UniProt or InterPro

Protein Sequence (618 amino acids)

>SO1168 penicillin-binding protein 2 (NCBI ptt file) (Shewanella oneidensis MR-1)
MSPKKRITMHDHAAEASLFKRRALFTFFCVVALLSMLVTNLYHLQVESYKDYATRSNDNR
IRVVPIAPSRGLIYDRNGVLLAENQPFYSLDLVPEKIANMSETLDELGKLIEISPDEREN
FTEALKFHRRFKPLTLKNQLTEEQVAIFSVNQHRFPGITVEAGLKRNYPYVSQLTHVLGY
VGKINTRDRAQLERNDQWKNYAATKDIGKQGIEKFYESLLHGTPGHLEEEVNNRGRTIRT
LKIVPPEPGQDIYLTLDLQLQQKAVELLQGHKGSIVAIDPRDGGILALVSSPSYDPNQFV
QGINRKDYSDLLNDKSRPLINRATQGQYAPASTVKPIIALLGLDEKAVTEHTRIWDPGFW
QIPGVERKYRDWKRWGHGWVNVYSAIVESCDTYFYELAYKIGVDPIARFMEQFGFGQNTG
VDIFEESTGNMPSKEWKRLKYNQAWYIGDTISVGIGQGYWTATPLQLASATAILANNGRR
FPPHLLKSIKDNTAKIDSPINELPPIELKNPRNWKIINEAMRQTAHKSRFTDASYTAAMK
TGTAQVIGVAENTKYDANKIAEHFRDNALVVAYAPFENPKIVLAVVMENAGWGGANAGPV
ARAMLDEYMLRDTWKPTP