Protein WP_048818108.1 in Desulfotomaculum hydrothermale Lam5
Annotation: NCBI__GCF_000315365.1:WP_048818108.1
Length: 221 amino acids
Source: GCF_000315365.1 in NCBI
Candidate for 25 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 52% | 160.6 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 52% | 160.6 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 45% | 50% | 159.1 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 41% | 51% | 153.3 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 52% | 151.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 44% | 52% | 149.8 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 38% | 56% | 146.7 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 38% | 56% | 146.7 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 53% | 146.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 39% | 53% | 145.6 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 39% | 52% | 145.2 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| sucrose catabolism | thuK | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 39% | 52% | 145.2 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 53% | 143.3 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-cellobiose catabolism | msiK | lo | MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 38% | 53% | 139.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 52% | 139.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 38% | 51% | 139.4 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 36% | 51% | 137.1 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 53% | 135.2 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 40% | 51% | 133.3 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 52% | 109.8 | ABC-type molybdate transporter (EC 7.3.2.5); ABC-type tungstate transporter (EC 7.3.2.6) | 42% | 177.2 |
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
MITMLEAFIQKKLWHFTLDFQVQINNEILVLWGPSGAGKTTILHCLAGLVKPSSGLIRLN
KQVLYSSEDKIHLSPQDRNVGYLFQDYALFPHMTVRQNVMYGLRSKKTFQSNINPVEILN
SFGVGHLTDRYPRQLSGGEKQRVALARALAVQPKLLLLDEPFSALDKSTKESLRQEVKKL
HRQWQIPFILVTHDEADTHYLGDRIISLNKGQPCQVVGKAN
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