Protein Pf1N1B4_4398 in Pseudomonas fluorescens FW300-N1B4
Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4398
Length: 232 amino acids
Source: pseudo1_N1B4 in FitnessBrowser
Candidate for 6 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artM | hi | AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) | 84% | 100% | 395.6 | OCM1 aka OccM, component of Octopine porter | 50% | 218.4 |
| L-citrulline catabolism | AO353_03045 | hi | ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) | 78% | 100% | 374.4 | ABC transporter for L-Arginine, permease component 1 | 51% | 218.8 |
| L-lysine catabolism | hisM | med | ABC transporter for L-Lysine, permease component 2 (characterized) | 50% | 97% | 216.1 | AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter | 84% | 395.6 |
| L-histidine catabolism | hisM | med | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 47% | 96% | 205.7 | AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter | 84% | 395.6 |
| L-citrulline catabolism | PS417_17600 | med | ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) | 46% | 92% | 194.5 | AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter | 84% | 395.6 |
| L-histidine catabolism | BPHYT_RS24010 | med | Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) | 41% | 92% | 177.9 | AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter | 84% | 395.6 |
Sequence Analysis Tools
View Pf1N1B4_4398 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
Fitness BLAST: loading...
Sequence
MILDYNLIWENLPLYFNGALLTLKVLFISLALGLVLAIPLALMRVSRSPLINFPAWLYTY
VIRGTPMLVQLFLIYYGLAQFEAVRQSVLWPYLSSATFCACLAFAINTSAYSAELLAGSL
KSTPHGEIEAAKAMGMSRLTLYRRILMPSALRRALPQYSNEVLMMLQTTSLASIVTLVDI
TGAARTVSSRFYLPFEAFITAGLIYLALTFILVRLFKLAERHWLAYLAPRKY
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