Protein BPHYT_RS07280 in Burkholderia phytofirmans PsJN
Annotation: FitnessBrowser__BFirm:BPHYT_RS07280
Length: 466 amino acids
Source: BFirm in FitnessBrowser
Candidate for 14 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-tryptophan catabolism | aroP | hi | Amino acid permease (characterized, see rationale) | 68% | 97% | 615.1 | L-alanine and D-alanine permease | 39% | 337.0 |
| D-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 39% | 93% | 337 | GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP | 38% | 329.3 |
| L-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 39% | 93% | 337 | GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP | 38% | 329.3 |
| L-threonine catabolism | RR42_RS28305 | lo | D-serine/D-alanine/glycine transporter (characterized, see rationale) | 39% | 97% | 334.3 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-proline catabolism | proY | lo | GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) | 38% | 97% | 329.3 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-histidine catabolism | permease | lo | histidine permease (characterized) | 38% | 97% | 323.6 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-phenylalanine catabolism | aroP | lo | Aromatic amino acid transport protein AroP (characterized, see rationale) | 36% | 97% | 313.9 | L-alanine and D-alanine permease | 39% | 337.0 |
| phenylacetate catabolism | H281DRAFT_04042 | lo | Aromatic amino acid transporter AroP (characterized, see rationale) | 35% | 98% | 302.4 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-tyrosine catabolism | aroP | lo | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 34% | 96% | 287.3 | L-alanine and D-alanine permease | 39% | 337.0 |
| D-serine catabolism | cycA | lo | DL-alanine permease SerP2 (characterized) | 30% | 98% | 220.3 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-arginine catabolism | rocE | lo | S-adenosylmethionine permease GAP4; SAM permease; Amino-acid permease GAP4 (characterized) | 33% | 73% | 218.8 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-serine catabolism | serP | lo | Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) | 30% | 98% | 218.8 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-tryptophan catabolism | TAT | lo | tryptophan permease (characterized) | 30% | 71% | 199.5 | L-alanine and D-alanine permease | 39% | 337.0 |
| L-lysine catabolism | lysP | lo | uncharacterized amino-acid permease C869.11 (characterized) | 30% | 69% | 187.6 | L-alanine and D-alanine permease | 39% | 337.0 |
Sequence Analysis Tools
View BPHYT_RS07280 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
Fitness BLAST: loading...
Sequence
MTQEQRGFDTIVEREKGLQRGLSTGQLSMIAIGGAIGTGLFLGSGFAIGFAGPSVLVSYA
IGALIALLLMGCLAEMTVAHPTSGSFGAYAEHYIAPWAGFLVRYAYWSSIVFAVGTEVTA
IAVYMKYWFPAVPGWYWIVGFSAALIGINSVSVKVFGAVEYVFSMLKIVAIVGFILLGAY
VVFGAPADSTIGFANYTSHGGFFPKGVWGMWVAVIVSIFSYLSIEMIAVAAGEARDPQKA
ITRAFRATMFRLVFFYLLTLALMLAIVPWNAAGTDESPFVRVMAATHVPGAAGVINFVIL
VAALSAMNSQLYITTRMMFSLSRAGYAPRKLGALNGKGVPVAALWLSTIGIALATVLNVV
YPDASFVLMMSVSMFGAMFTWLMIFVTHFFFRHRHQGAPLAFRMWGYPGTSALGAGLMVS
ALVTTWFTREFRMTLVIGVPFIVSLLVVYFVWYRKRAVEGAAAELA
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:
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