Protein RR42_RS28305 in Cupriavidus basilensis 4G11
Annotation: FitnessBrowser__Cup4G11:RR42_RS28305
Length: 472 amino acids
Source: Cup4G11 in FitnessBrowser
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-threonine catabolism | RR42_RS28305 | hi | D-serine/D-alanine/glycine transporter (characterized, see rationale) | 100% | 100% | 937.9 | L-alanine and D-alanine permease | 55% | 519.2 |
| D-alanine catabolism | cycA | hi | L-alanine and D-alanine permease (characterized) | 55% | 96% | 519.2 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 45% | 427.6 |
| L-alanine catabolism | cycA | hi | L-alanine and D-alanine permease (characterized) | 55% | 96% | 519.2 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 45% | 427.6 |
| D-serine catabolism | cycA | med | D-serine/D-alanine/glycine transporter (characterized) | 46% | 99% | 439.5 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-phenylalanine catabolism | aroP | med | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 45% | 99% | 427.6 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-tryptophan catabolism | aroP | med | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 45% | 99% | 427.6 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-tyrosine catabolism | aroP | med | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 45% | 99% | 427.6 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-histidine catabolism | permease | med | histidine permease (characterized) | 46% | 94% | 423.7 | L-alanine and D-alanine permease | 55% | 519.2 |
| phenylacetate catabolism | H281DRAFT_04042 | med | Aromatic amino acid transporter AroP (characterized, see rationale) | 45% | 97% | 422.2 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-proline catabolism | proY | med | Proline-specific permease (ProY) (characterized) | 43% | 98% | 421.8 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-asparagine catabolism | ansP | med | Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) | 45% | 93% | 413.7 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-lysine catabolism | lysP | lo | The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) | 38% | 97% | 328.9 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-arginine catabolism | rocE | lo | Amino-acid permease RocE (characterized) | 37% | 95% | 311.2 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-serine catabolism | serP | lo | Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) | 37% | 100% | 291.6 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-threonine catabolism | serP1 | lo | Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) | 37% | 100% | 291.6 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-isoleucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 30% | 87% | 217.2 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-leucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 30% | 87% | 217.2 | L-alanine and D-alanine permease | 55% | 519.2 |
| L-valine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 30% | 87% | 217.2 | L-alanine and D-alanine permease | 55% | 519.2 |
Sequence Analysis Tools
View RR42_RS28305 at FitnessBrowser
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
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Sequence
MTDVRKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSY
AIGGVAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEIT
AVAVYVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGL
AIIFFGVTPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNP
EKVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNL
VVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLL
NYIVPEQVFVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLV
VAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFTKSRALLEGHVQKSA
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