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
Predict protein localization: PSORTb
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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:
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