Finding step livF for L-valine catabolism in Limnohabitans curvus MWH-C5
5 candidates for livF: L-valine ABC transporter, ATPase component 1 (LivF/BraG)
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| hi | B9Z44_RS05720 | ABC transporter ATP-binding protein | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 54% | 99% | 258.1 | Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 51% | 227.6 |
| hi | B9Z44_RS04210 | ABC transporter ATP-binding protein | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 54% | 99% | 255 | Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 53% | 230.7 |
| hi | B9Z44_RS08450 | ABC transporter ATP-binding protein | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 47% | 99% | 221.1 | Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 45% | 184.9 |
| hi | B9Z44_RS10005 | ABC transporter ATP-binding protein | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 45% | 99% | 210.7 | Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW | 45% | 193.4 |
| hi | B9Z44_RS09920 | ABC transporter ATP-binding protein | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 45% | 92% | 195.3 | NatE, 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) | 42% | 185.3 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
Definition of step livF
- Curated sequence CH_003736: high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF. LivF aka B3454, component of Leucine; leucine/isoleucine/valine porter. branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF (EC 7.4.2.2). branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF (EC 7.4.2.2)
- Curated sequence P21630: High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine
- Curated sequence Q8DQH7: ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM
- UniProt sequence Q1MCU3: SubName: Full=ATP-binding component of a broad range amino acid ABC transporter {ECO:0000313|EMBL:CAK09237.1};
- Comment: ABC transporters with 5 components: E. coli livFGHMJ and related systems (but the alternate substrate-binding protein livK does not transport valine). Related systems include livJFGHM from Streptococcus pneumoniae, braCDEFG from Pseudomonas aeruginosa (braC is the SBP), and braCDEFG or braC3/braDEFG from R. leguminosarum. In R. leguminosarum, the proximal braC (Q9L3M3) transports leucine (PMC135202), and likely valine as well. braC3 (RL3540; Q1MDE9) is a secondary SBP that transports leucine/isoleucine/valine/alanine (PMID:19597156). LivH/BraD = RL3750/Q1MCU0; LivM/BraE = RL3749/Q1MCU1; LivG/BraF = RL3748/Q1MCU2; LivF/BraG = RL3747/Q1MCU3. (The related liv system from Acidovorax, Ac3H11_1692:1695 and Ac3H11_2396, has not been shown to transport valine.)
Or cluster all characterized livF proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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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