Protein WP_004107105.1 in Rhizobium freirei PRF 81
Annotation: NCBI__GCF_000359745.1:WP_004107105.1
Length: 474 amino acids
Source: GCF_000359745.1 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-arginine catabolism | braE | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-glutamate catabolism | braE | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-histidine catabolism | braE | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-isoleucine catabolism | livM | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC | 33% | 146.4 |
| L-leucine catabolism | livM | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC | 33% | 146.4 |
| L-valine catabolism | livM | hi | Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) | 77% | 100% | 704.1 | BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC | 33% | 146.4 |
| D-alanine catabolism | AZOBR_RS08240 | hi | Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) | 42% | 95% | 349 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-proline catabolism | AZOBR_RS08240 | hi | Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) | 42% | 95% | 349 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-alanine catabolism | braE | hi | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 46% | 100% | 335.1 | High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M | 44% | 284.3 |
| L-serine catabolism | braE | hi | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 46% | 100% | 335.1 | High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M | 44% | 284.3 |
| L-threonine catabolism | braE | hi | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 46% | 100% | 335.1 | High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M | 44% | 284.3 |
| L-phenylalanine catabolism | livM | hi | High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) | 46% | 100% | 334.3 | BraE aka Bra2E, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC | 33% | 146.4 |
| L-proline catabolism | HSERO_RS00890 | med | ABC transporter ATP-binding protein (characterized, see rationale) | 43% | 94% | 250.4 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-serine catabolism | Ac3H11_1694 | med | ABC transporter ATP-binding protein (characterized, see rationale) | 43% | 94% | 250.4 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
| L-tyrosine catabolism | Ac3H11_1694 | med | ABC transporter ATP-binding protein (characterized, see rationale) | 43% | 94% | 250.4 | High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine | 48% | 315.5 |
Sequence Analysis Tools
View WP_004107105.1 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
MANSNFVAGKAAPGLVQKGITDAFWTALIAFGMFVLYIGLKTDQNIDNKLIIVQRWGLLA
IIVAIAAAGRFVMTVFVQPALAARKAARAKVAPVEAEAGFIGRNFTKIALLLLLVYPLAA
VAIFGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSM
HFGLSFWILLPLSGMLAGLWGMILGFPVLRLRGDYLAIVTLAFGEIIRIVLTNWTDFTQG
SFGISNITKASLFGFYTFDLKDPHNLIRTLGLPISSAWYKIFLFYVILGLCMLTAYVTIR
LRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFGGFAGSFFAARQGFVSPES
FVFLESAVILAIVVLGGMGSLKGIAIAAIAMVGGTEVLRNMSFLKTGLVFGDTTIIPGFG
PDFTPELYRMLIFGLAMVVVMIFKPRGFVGTREPTAFLKERKAVSGSFTKEGHG
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