Protein YP_004139781.1 in Mesorhizobium ciceri WSM1271
Annotation: NCBI__GCF_000185905.1:YP_004139781.1
Length: 300 amino acids
Source: GCF_000185905.1 in NCBI
Candidate for 15 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-isoleucine catabolism | livH | hi | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 41% | 100% | 231.1 | L-proline and D-alanine ABC transporter, permease component 1 | 36% | 204.1 |
| L-leucine catabolism | livH | hi | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 41% | 100% | 231.1 | L-proline and D-alanine ABC transporter, permease component 1 | 36% | 204.1 |
| L-valine catabolism | livH | hi | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 41% | 100% | 231.1 | L-proline and D-alanine ABC transporter, permease component 1 | 36% | 204.1 |
| L-proline catabolism | HSERO_RS00885 | lo | ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) | 39% | 97% | 217.6 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-phenylalanine catabolism | livH | lo | ABC transporter permease (characterized, see rationale) | 38% | 97% | 207.2 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-serine catabolism | Ac3H11_1695 | lo | ABC transporter permease (characterized, see rationale) | 38% | 97% | 207.2 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-tyrosine catabolism | Ac3H11_1695 | lo | ABC transporter permease (characterized, see rationale) | 38% | 97% | 207.2 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| D-alanine catabolism | AZOBR_RS08235 | lo | L-proline and D-alanine ABC transporter, permease component 1 (characterized) | 36% | 99% | 204.1 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-proline catabolism | AZOBR_RS08235 | lo | L-proline and D-alanine ABC transporter, permease component 1 (characterized) | 36% | 99% | 204.1 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-arginine catabolism | braD | lo | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 99% | 195.3 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-glutamate catabolism | braD | lo | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 99% | 195.3 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-histidine catabolism | braD | lo | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 34% | 99% | 195.3 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-alanine catabolism | braD | lo | High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 34% | 99% | 194.9 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-serine catabolism | braD | lo | High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 34% | 99% | 194.9 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
| L-threonine catabolism | braD | lo | High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 34% | 99% | 194.9 | ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM | 41% | 231.1 |
Sequence Analysis Tools
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
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Sequence
MTQLDYILQQIVNAVSLGSLYALVAVGLSIVFGVLKLTNFAHGDVMMVGAFGVALLVGIG
VPFPVAVICGIAAAAVAGFLIERIAYRPIRDAPDVARLLTSLAVTYIIENVGILVFTSSP
RNFPLPDILNTSWEMSNGAITFTSINLLTIALTFVSLLLLGWFITRTTTGLGMRAAAEDM
SAAHLVGLNVNRLIIVAFIVASAYAGLAGILWAAQAGVVQPQMGFTPLLKAFVAAIIGGF
GSIAGALVGGYILGALEIFIVAFLPSSVSSYRDAIVFAVLIAFLLVRPGGLLQPNREIKL
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