Protein Info for GFF2024 in Sphingobium sp. HT1-2

Annotation: Rhamnogalacturonan endolyase (EC 4.2.2.23)

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 50 100 150 200 250 300 350 400 450 500 550 600 639 signal peptide" amino acids 1 to 25 (25 residues), see Phobius details PF18370: RGI_lyase" amino acids 33 to 104 (72 residues), 69.7 bits, see alignment E=4.4e-23 PF21348: RGL11_C" amino acids 118 to 251 (134 residues), 229.8 bits, see alignment E=1.3e-71 amino acids 258 to 635 (378 residues), 545.4 bits, see alignment E=2.7e-167

Best Hits

KEGG orthology group: None (inferred from 66% identity to cse:Cseg_2735)

Predicted SEED Role

"Predicted rhamnogalacturonan lyase in rhamnose utilization cluster" in subsystem L-rhamnose utilization

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

Find the best match in UniProt

Protein Sequence (639 amino acids)

>GFF2024 Rhamnogalacturonan endolyase (EC 4.2.2.23) (Sphingobium sp. HT1-2)
MQMHTTIRAFTMTLGLATSTMALATGPTARIAAERLDRGAVALPAQGGGMLITWRLLADD
PATIRFRLLRDGKPIHDSRVGEATAFVDKKGSATSRYAVQPMGDKSAPSPAMMWDKSYLS
IPLTPPADGVTPAGESFSYTANDASAADLDGDGRYEIILKWDPTNSHDNSQGGYSGPVLL
DAYRLDGTRLWRIDLGRNIRAGAHYTQFLAFDFDGDGRAEVAMKTADGTVDGTGTVIGDA
KADWRGHDGEVPQRDRTGAKILPDGTKVAPMQGRIVKGPEYLTVFDGLTGKALATAPYDP
PRYPGGNPTTEQLTESWGDAYANRSDRFLAGVAYLDGHLPSMVFGRGYYARTAIAAWDWR
DGKLTQRWLFDSSQPGKGDYAGRGNHQLSIADVDGDGRDEVIYGSMAVDDDGKGLWTQPL
FHGDTMHVSDLDPARPGLEKFGVFEDQRQNGMIGSALLDARTGQMLWSTPAEKDTGRGVA
ADIDPRHWGAEFWNSSSAELFDVAGKPIGPRPRQMNFAIWWDGDLLRELLDKTTISKWDW
ENGKEIPLLSPEGLSSNNGTKATPALQADLIGDWREEVVWRSADNRELRIYTTPYPTTHR
FVTLMQDPVYRLGVAWQNTAYNQPPHTSFYLGAGKQGER