Protein 350994 in Bacteroides thetaiotaomicron VPI-5482
Annotation: FitnessBrowser__Btheta:350994
Length: 238 amino acids
Source: Btheta in FitnessBrowser
Candidate for 16 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 79% | 146 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 79% | 146 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 60% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 60% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 42% | 60% | 144.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 40% | 57% | 140.2 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 64% | 139 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 36% | 54% | 136.3 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 62% | 136 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 62% | 136 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 37% | 54% | 132.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 57% | 119.4 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 32% | 86% | 119 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 85% | 115.9 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 73% | 114.8 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 53% | 104 | Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- | 46% | 211.1 |
Sequence Analysis Tools
View 350994 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MIKTEKLSMLFTTEEVQTKALNEVTLHVEQGEFVAIMGPSGCGKSTLLNILGTLDSPTSG
SYFFEGKQVDKMNENQLTALRKNNLGFIFQSFNLIDELTVYENVELPLVYMGIKTAQRKE
KVNKVLEKVNLLHRANHYPQQLSGGQQQRVAIARAVVTDCKLLLADEPTGNLDSVNGVEV
MELLSELNRQGTTIIIVTHSQRDATYAHRIIRLLDGQIVSENINRPLEKSTSSKNEAV
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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