Protein GFF558 in Pseudomonas stutzeri RCH2
Annotation: FitnessBrowser__psRCH2:GFF558
Length: 232 amino acids
Source: psRCH2 in FitnessBrowser
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-isoleucine catabolism | livF | med | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 42% | 96% | 172.9 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-phenylalanine catabolism | livF | med | High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) | 42% | 96% | 172.9 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-proline catabolism | HSERO_RS00900 | med | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 43% | 94% | 172.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-alanine catabolism | braG | med | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 43% | 93% | 171.8 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-leucine catabolism | livF | med | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 43% | 93% | 171.8 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-serine catabolism | braG | med | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 43% | 93% | 171.8 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-threonine catabolism | braG | med | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 43% | 93% | 171.8 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-valine catabolism | livF | med | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 43% | 93% | 171.8 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-arginine catabolism | braG | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 42% | 91% | 169.1 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-glutamate catabolism | braG | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 42% | 91% | 169.1 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-histidine catabolism | braG | med | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 42% | 91% | 169.1 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| D-alanine catabolism | AZOBR_RS08250 | med | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 41% | 95% | 167.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-proline catabolism | AZOBR_RS08250 | med | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 41% | 95% | 167.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 93% | 162.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 93% | 162.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 39% | 89% | 150.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 39% | 89% | 150.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 39% | 89% | 150.2 | UrtE, component of The high-affinity (<1 μM) urea porter | 48% | 194.5 |
Sequence Analysis Tools
View GFF558 at FitnessBrowser
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
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Sequence
MLQVQQLHQYYGGSHILRGLSFEAKVGEVTCLLGRNGVGKTTLLKCLMGLIPAKEGAVNW
EGKPITGFKPHQRVHAGIAYVPQGREIFGRLTVEENLLMGLSRFSAREAKEVPEFIYELF
PVLKEMKHRRGGDLSGGQQQQLAIGRALASKPRLLILDEPTEGIQPSVIKEIGAVIRKLA
ARGDMAILLVEQFYDFAAELADQYLVMSRGEIIQQGRGENMAADGVQRLVAI
This GapMind analysis is from Sep 17 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