Protein WP_051305489.1 in Desulfobulbus mediterraneus DSM 13871
Annotation: NCBI__GCF_000429965.1:WP_051305489.1
Length: 383 amino acids
Source: GCF_000429965.1 in NCBI
Candidate for 21 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-xylose catabolism | xylH | hi | D-xylose ABC transporter, permease protein (characterized) | 45% | 92% | 302.8 | Probable ABC transport system permease protein for sugars, component of ABC sugar transporter that plays a role in the probiotic benefits through acetate production | 37% | 242.3 |
| L-arabinose catabolism | gguB | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-cellobiose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-galactose catabolism | gguB | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-glucose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| lactose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-maltose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| sucrose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| trehalose catabolism | mglC | med | GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 41% | 95% | 265.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-ribose catabolism | rbsC | lo | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 37% | 93% | 198 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-fructose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 39% | 77% | 161.8 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| sucrose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 39% | 77% | 161.8 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| xylitol catabolism | PS417_12060 | lo | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 36% | 81% | 160.6 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| myo-inositol catabolism | PS417_11895 | lo | m-Inositol ABC transporter, permease component (iatP) (characterized) | 36% | 92% | 156.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| L-fucose catabolism | HSERO_RS05255 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 34% | 82% | 154.8 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-mannose catabolism | HSERO_RS03645 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 34% | 90% | 154.8 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-xylose catabolism | xylF_Tm | lo | ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) | 33% | 95% | 145.2 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| D-galactose catabolism | BPHYT_RS16925 | lo | Arabinose ABC transporter permease (characterized, see rationale) | 42% | 51% | 139.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| L-fucose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 31% | 74% | 104.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| L-rhamnose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 31% | 74% | 104.4 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
| L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 33% | 71% | 95.9 | D-xylose ABC transporter, permease protein | 45% | 302.8 |
Sequence Analysis Tools
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...
Sequence
MATAVNSANPFHHVAGFLKENGTLVALVALALIFSLMDEAFFTPRNLTNLARQTTIIGII
SVGMTMVIIINGIDLSVGSIVGLSAIVVTLLMQQGMNVWLAIPLTLLTTGTLIGLWNGFW
IAHYNIPPFIITLGMMTIARGLALTLSNGSSVPVTDPIFPQLGGSYIPPAVSGILIILTL
SLFIFALFREVGQRRKYGAVVKLQPLIASTLITVVGLGLSFYVFTTYRGIPYPVAVFSII
AFIGIFMLNNTIFGRRIYAIGGNEEAARLSGIRIYRVKLIVYSIITTLAALSGVLLASRL
NGASPNLGNMFELDAISAVIIGGTSFSGGVGTISGTVIGAFIIGILNNGMSLLGVPTFYQ
LIIKGLIIILAVWFDVLNKKKSA
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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