Annotation: NCBI__GCF_001931675.1:WP_047212605.1
Length: 316 amino acids
Source: GCF_001931675.1 in NCBI
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
---|---|---|---|---|---|---|---|---|---|
D-mannose catabolism | TM1748 | lo | TM1748, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 34% | 93% | 167.5 | dipeptide ABC transporter, permease protein DppC | 41% | 233.0 |
D-cellobiose catabolism | TM0029 | lo | TM0029, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 79% | 120.2 | dipeptide ABC transporter, permease protein DppC | 41% | 233.0 |
View WP_047212605.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MGLGQVSVSVAAGKSLLSRCRDSDLFHSFVRSPLAMVAALIACVMIVAAVFAPWVAPHHP FDLSTLNLNNALLPPAWVSHGQWTFFLGTDDQGRDVLSAIIYGSRISLFIGVVAVLLSLV FGVGLGLLSGFSGGALDAVIMRVADVQLSFPSILIALLVDGIARAIFPHELHDLIAFPVL ILSISLAGWPQYARTVRGSTLVEKHKEYVQAARVMGISSPRIMFRHVLPNVLGPVLVLAT VHVATAIITEATLSFLGVGVSPTSPSLGTLIRTGNDYLFSGEWWITIFPGLALVLLVLSV NLLGDWLRDALNPKLQ
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory