Protein WP_013706789.1 in Desulfobacca acetoxidans DSM 11109
Annotation: NCBI__GCF_000195295.1:WP_013706789.1
Length: 257 amino acids
Source: GCF_000195295.1 in NCBI
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-alanine catabolism | braF | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 51% | 242.3 |
| L-isoleucine catabolism | livG | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 45% | 211.5 |
| L-leucine catabolism | livG | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 45% | 211.5 |
| L-serine catabolism | braF | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 51% | 242.3 |
| L-threonine catabolism | braF | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 51% | 242.3 |
| L-valine catabolism | livG | hi | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 54% | 98% | 268.5 | Putative branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 45% | 211.5 |
| L-phenylalanine catabolism | livG | hi | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 54% | 98% | 267.7 | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 51% | 242.3 |
| L-proline catabolism | HSERO_RS00895 | med | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 51% | 97% | 246.9 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| D-alanine catabolism | AZOBR_RS08245 | med | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 50% | 89% | 239.2 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-proline catabolism | AZOBR_RS08245 | med | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 50% | 89% | 239.2 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-serine catabolism | Ac3H11_1693 | med | ABC transporter ATP-binding protein (characterized, see rationale) | 48% | 96% | 237.3 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-tyrosine catabolism | Ac3H11_1693 | med | ABC transporter ATP-binding protein (characterized, see rationale) | 48% | 96% | 237.3 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-arginine catabolism | braF | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 47% | 90% | 219.5 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-glutamate catabolism | braF | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 47% | 90% | 219.5 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-histidine catabolism | braF | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 47% | 90% | 219.5 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-isoleucine catabolism | natA | med | 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) | 42% | 96% | 195.7 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-leucine catabolism | natA | med | 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) | 42% | 96% | 195.7 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-proline catabolism | natA | med | 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) | 42% | 96% | 195.7 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-valine catabolism | natA | med | 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) | 42% | 96% | 195.7 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| L-histidine catabolism | natA | med | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 42% | 93% | 195.3 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| D-lactate catabolism | PGA1_c12640 | med | D-lactate transporter, ATP-binding component (characterized) | 41% | 99% | 194.1 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 33% | 90% | 137.5 | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine | 54% | 268.5 |
Sequence Analysis Tools
View WP_013706789.1 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
MLLEINNLSKSFGGLQALNGVTFDVRMGVVQALIGPNGAGKTTCFNLISGILPPSSGSIR
LDGRELSYLPPHRIARLGLARTFQNIQLFSGLSVLENVLVGQHLHLHGNLLATLLNLPAV
RRQERRSADFARELLDFVGLADKEHWAADSLAYGDQRRLEIARAMALNPRLLLLDEPAAG
MNPRETEDLMALIDNIQQRHITVLLIEHDMNLVMNISSRIVVFDQGRVIAQGPPKAIRQN
PQVIEAYLGREEEDGDV
This GapMind analysis is from Sep 24 2021. 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