Protein 353166 in Bacteroides thetaiotaomicron VPI-5482
Annotation: FitnessBrowser__Btheta:353166
Length: 218 amino acids
Source: Btheta in FitnessBrowser
Candidate for 40 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 42% | 90% | 171.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 40% | 90% | 153.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 37% | 89% | 150.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 37% | 89% | 150.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 37% | 56% | 148.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 36% | 83% | 147.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 90% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 90% | 147.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 61% | 146 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-histidine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 36% | 87% | 145.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 35% | 63% | 144.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 59% | 142.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 58% | 141 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 35% | 82% | 139.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 34% | 87% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 58% | 137.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 33% | 57% | 136.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 77% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 77% | 121.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 86% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 90% | 107.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 90% | 107.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| D-lactate catabolism | PGA1_c12640 | lo | D-lactate transporter, ATP-binding component (characterized) | 31% | 89% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-alanine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-histidine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-leucine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-proline catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-serine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-threonine catabolism | braF | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 78% | 101.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 32% | 89% | 100.1 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 88% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 88% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 88% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 88% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 88% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 50% | 207.6 |
Sequence Analysis Tools
View 353166 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAI
DGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAME
ILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLF
FDLRDRLGQTFVIVTHDEGLAKITDRTVHMVDGTIKKD
This GapMind analysis is from Apr 09 2024. 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:
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