Protein WP_026329578.1 in Thiomicrorhabdus arctica DSM 13458
Annotation: NCBI__GCF_000381085.1:WP_026329578.1
Length: 271 amino acids
Source: GCF_000381085.1 in NCBI
Candidate for 32 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 40% | 85% | 147.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 98% | 147.1 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 98% | 147.1 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-glutamate catabolism | gltL | lo | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 37% | 98% | 147.1 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 85% | 146.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 85% | 146.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 39% | 80% | 145.2 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 37% | 86% | 144.8 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-asparagine catabolism | aapP | lo | 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) | 37% | 86% | 144.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-aspartate catabolism | aapP | lo | 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) | 37% | 86% | 144.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-glutamate catabolism | aapP | lo | 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) | 37% | 86% | 144.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-leucine catabolism | aapP | lo | 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) | 37% | 86% | 144.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-proline catabolism | aapP | lo | 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) | 37% | 86% | 144.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 91% | 138.7 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 91% | 138.7 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 34% | 66% | 137.1 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-alanine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-isoleucine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-leucine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-proline catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-serine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-threonine catabolism | braF | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-valine catabolism | natA | lo | NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 33% | 88% | 131.3 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 38% | 88% | 129.4 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-isoleucine 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| 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) | 33% | 94% | 112.5 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 94% | 110.2 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 58% | 99.8 | phosphonates transport atp-binding protein phnc; EC 3.6.3.28 | 43% | 176.0 |
Sequence Analysis Tools
View WP_026329578.1 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
MLIFDHVSRIYPDGTQAVKDVSVQLKQGEFCVLLGPSGAGKSTLMNMVNGLVEPTSGKII
LDGELLTKKNLQMIQRSVSMIHQQLYLVPRLSVLHNVLTGILPLAGFWRSMVKSFPIKDQ
RRAYELLSEVGLKEKHLMRRASELSGGQQQRVAIARAFMASPKLVLADEPVASLDPTMSR
SVLNSLKTAAQTNGATVLCTLHQMDYALEFADRIIALRDGEVFFDGPPSAMDADVQRRLY
EIEHDNLEKQQAEPVEKPTRPLLVDIKEAVA
This GapMind analysis is from Apr 09 2024. 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