Protein WP_012400013.1 in Paraburkholderia phymatum STM815
Annotation: NCBI__GCF_000020045.1:WP_012400013.1
Length: 466 amino acids
Source: GCF_000020045.1 in NCBI
Candidate for 20 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| phenylacetate catabolism | H281DRAFT_04042 | hi | Aromatic amino acid transporter AroP (characterized, see rationale) | 88% | 100% | 820.8 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-phenylalanine 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) | 70% | 99% | 652.1 | L-tyrosine transporter | 64% | 629.8 |
| 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) | 70% | 99% | 652.1 | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs | 60% | 570.1 |
| 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) | 70% | 99% | 652.1 | Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs | 60% | 570.1 |
| L-threonine catabolism | RR42_RS28305 | med | D-serine/D-alanine/glycine transporter (characterized, see rationale) | 45% | 96% | 415.6 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| D-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 43% | 97% | 399.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-alanine catabolism | cycA | med | L-alanine and D-alanine permease (characterized) | 43% | 97% | 399.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-histidine catabolism | permease | med | histidine permease (characterized) | 43% | 94% | 396.4 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-proline catabolism | proY | med | Proline-specific permease (ProY) (characterized) | 44% | 100% | 395.6 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| D-serine catabolism | cycA | med | D-serine/D-alanine/glycine transporter (characterized) | 40% | 97% | 367.1 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-serine catabolism | serP | med | 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) | 41% | 79% | 289.7 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-threonine catabolism | serP1 | med | 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) | 41% | 79% | 289.7 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-asparagine catabolism | ansP | lo | L-asparagine permease; L-asparagine transport protein (characterized) | 35% | 92% | 331.6 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-lysine catabolism | lysP | lo | The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) | 36% | 97% | 309.7 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-arginine catabolism | rocE | lo | Amino-acid permease RocE (characterized) | 35% | 100% | 308.5 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-isoleucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 35% | 79% | 232.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-leucine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 35% | 79% | 232.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-valine catabolism | Bap2 | lo | Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) | 35% | 79% | 232.3 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-asparagine catabolism | AGP1 | lo | general amino acid permease AGP1 (characterized) | 32% | 76% | 229.9 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
| L-tryptophan catabolism | TAT | lo | tryptophan permease (characterized) | 32% | 71% | 209.9 | Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan | 70% | 652.1 |
Sequence Analysis Tools
View WP_012400013.1 at NCBI
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
MSNAGNNGQQHDGLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIGGF
IAFLIMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTY
VHFWWPGVPAWLSALVCFVVINAINLANVKAYGETEFWFAIVKVVAVMGMIVFGGYLLLS
GHGGPQASISNLWSQGGFFPHGVHGLFMMLAVIMFSFGGLELIGITAAEADDPQKSIPKA
VNQVIYRILIFYICSLIVLLSLYPWNQVAEGGSPFVMIFSQIGAGLTANVLNVVVLTAAL
SVYNSGVYANSRMLYGLAEQGNAPRALLEVDRRGVPYMAIGLSAVATFACVIINYLMPAK
ALDVLMALVVAALVLNWSLISLTHLKSRRAMLAQGDTLVFKSLWFPLGNWVCLAFMALIL
VILALTPGLNVSVLLVPVWLFVMWIGYVVKRRRATAHQLAGATGGR
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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