Protein RR42_RS33495 in Cupriavidus basilensis 4G11
Annotation: RR42_RS33495 aromatic amino acid transporter
Length: 465 amino acids
Source: Cup4G11 in FitnessBrowser
Candidate for 16 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-phenylalanine catabolism | aroP | hi | Aromatic amino acid transport protein AroP (characterized, see rationale) | 100% | 100% | 918.7 | L-tyrosine transporter | 63% | 596.7 |
| L-tryptophan catabolism | aroP | hi | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 71% | 98% | 647.9 | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs | 62% | 580.5 |
| L-tyrosine catabolism | aroP | hi | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized) | 71% | 98% | 647.9 | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs | 62% | 580.5 |
| phenylacetate catabolism | H281DRAFT_04042 | med | Aromatic amino acid transporter AroP (characterized, see rationale) | 67% | 97% | 632.5 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-threonine catabolism | RR42_RS28305 | med | D-serine/D-alanine/glycine transporter (characterized, see rationale) | 43% | 96% | 415.2 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| D-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 43% | 95% | 404.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 43% | 95% | 404.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-proline catabolism | proY | med | Proline-specific permease (ProY) (characterized) | 46% | 98% | 396.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-histidine catabolism | permease | med | histidine permease (characterized) | 42% | 97% | 378.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| D-serine catabolism | cycA | med | D-serine/D-alanine/glycine transporter (characterized) | 41% | 98% | 365.2 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-asparagine catabolism | ansP | lo | Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) | 37% | 89% | 329.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-lysine catabolism | lysP | lo | Lysine permease LysP (characterized) | 37% | 94% | 296.2 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-serine catabolism | serP | lo | Serine permease SerP1 (characterized) | 36% | 96% | 293.1 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| 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% | 87% | 287.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-arginine catabolism | rocE | lo | Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized) | 33% | 77% | 241.5 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
| L-asparagine catabolism | AGP1 | lo | general amino acid permease AGP1 (characterized) | 31% | 69% | 209.5 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 71% | 647.9 |
Sequence Analysis Tools
View RR42_RS33495 at FitnessBrowser
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the SEED with FIGfam search
Fitness BLAST: loading...
Sequence
MVPNASDNTDATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGII
AFFIMRQLGEMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYV
QYWWPHIPTWASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASG
TAGPQASVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKAT
NQVIYRILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALS
VYNSGVYCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEA
FELLMGLVVSALIINWAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILY
VMYLTPGLRISVYLIPAWLAVLGLSYRLRQKQKRAEPALPERVSA
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