Protein BPHYT_RS31940 in Burkholderia phytofirmans PsJN
Annotation: FitnessBrowser__BFirm:BPHYT_RS31940
Length: 294 amino acids
Source: BFirm in FitnessBrowser
Candidate for 8 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | HSERO_RS00885 | med | ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) | 30% | 98% | 148.7 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 30% | 145.2 |
| L-isoleucine catabolism | livH | med | Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) | 30% | 96% | 147.1 | NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) | 31% | 139.8 |
| L-phenylalanine catabolism | livH | med | Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) | 30% | 96% | 147.1 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 30% | 145.2 |
| L-arginine catabolism | braD | med | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 99% | 146.4 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 30% | 145.2 |
| L-glutamate catabolism | braD | med | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 99% | 146.4 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 30% | 145.2 |
| L-histidine catabolism | braD | med | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 99% | 146.4 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 30% | 145.2 |
| L-leucine catabolism | livH | med | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 99% | 146.4 | NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) | 31% | 139.8 |
| L-valine catabolism | livH | med | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 99% | 146.4 | NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) | 31% | 139.8 |
Sequence Analysis Tools
View BPHYT_RS31940 at FitnessBrowser
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
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Sequence
MALIVQLALNTLQAGSVYVLFALGLTLIFGVMGVVNFAHGQFFTLGALLTSVLVPALREA
FGMGVALAFTFASAISIVAVLALAALVYQFGFRHYLRDTVGSFILSVGLLLFFEGVFLWV
FGGVPRVVPNIAPGELRVFGAAIELQRLVVFAIAVIITVLLYLMLAFTRFGRAIRATADD
AGAATLQGIRDKRTLLYGFMVGSFLSAVSGCLTAPIAVITPAVGNDYLIKGFITIIIGGL
GSVPGAIFGGLTIALIESVVGYYFDGTMATIGMFCVVALLLLIRPQGMLGHVQH
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