Protein WP_039104485.1 in Frischella perrara PEB0191
Annotation: NCBI__GCF_000807275.1:WP_039104485.1
Length: 242 amino acids
Source: GCF_000807275.1 in NCBI
Candidate for 33 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | hi | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 67% | 100% | 335.5 | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) | 46% | 213.0 |
| L-asparagine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-aspartate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-glutamate catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-histidine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-leucine catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-proline catabolism | aapP | med | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 46% | 93% | 215.3 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 46% | 90% | 212.6 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 46% | 90% | 212.6 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-glutamate catabolism | gltL | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 46% | 90% | 212.6 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 47% | 100% | 212.2 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 47% | 100% | 212.2 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 48% | 93% | 212.2 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-lysine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 48% | 93% | 212.2 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-citrulline catabolism | PS417_17605 | med | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 43% | 90% | 209.1 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 47% | 90% | 207.6 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 47% | 90% | 207.6 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 40% | 98% | 201.4 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-isoleucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 32% | 99% | 114.8 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-phenylalanine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 32% | 99% | 114.8 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-alanine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 91% | 110.5 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-leucine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 91% | 110.5 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-serine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 91% | 110.5 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-threonine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 91% | 110.5 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-valine catabolism | livF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 32% | 91% | 110.5 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 31% | 85% | 100.9 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 91% | 99 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 91% | 99 | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- | 67% | 335.5 |
Sequence Analysis Tools
View WP_039104485.1 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
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Sequence
MNIELSHINCFYGSHQALYDISICYPLGETIVLLGPSGAGKSSLLKVFNLLEVPVSGEMT
IADIHLDFQQKPAEELVRTLRRDVGIVFQNYNLWPHLTVLDNLIEAPCQVLKMSKAQATA
KALKILQRLKIDSMANRYPLHLSGGQQQRVAIARALMMEPKILLFDEPTAALDPEITSQV
ADIINELSETGITQIIVTHEVDFAKKVASQVIYMEKGKIIEQGDKTCFIHPLSKQFQAYL
SH
This GapMind analysis is from Sep 24 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