Protein GFF4002 in Pseudomonas stutzeri RCH2
Annotation: FitnessBrowser__psRCH2:GFF4002
Length: 419 amino acids
Source: psRCH2 in FitnessBrowser
Candidate for 8 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-glutamate catabolism | gltP | hi | Na+/H+ dicarboxylate symporter (characterized, see rationale) | 100% | 100% | 782.7 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 35% | 257.7 |
| L-asparagine catabolism | glt | hi | Sodium:dicarboxylate symporter (characterized, see rationale) | 46% | 94% | 356.3 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 35% | 257.7 |
| L-aspartate catabolism | glt | hi | Sodium:dicarboxylate symporter (characterized, see rationale) | 46% | 94% | 356.3 | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up | 35% | 257.7 |
| L-malate catabolism | dctA | lo | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) | 35% | 95% | 257.7 | Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter | 47% | 346.7 |
| fumarate catabolism | dctA | lo | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) | 35% | 95% | 257.7 | Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter | 47% | 346.7 |
| succinate catabolism | dctA | lo | The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) | 35% | 95% | 257.7 | Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter | 47% | 346.7 |
| acetate catabolism | dctA | lo | Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) | 31% | 92% | 228 | Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter | 47% | 346.7 |
| L-alanine catabolism | SLC1A4 | lo | neutral amino acid transporter A (characterized) | 38% | 52% | 187.2 | Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter | 47% | 346.7 |
Sequence Analysis Tools
View GFF4002 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
MTQSTTLSAPLRLLVRLPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIV
PLVFVSLVAGITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVAS
GNEQAKQAPSLVSILVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLF
DALAETFYKLTDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVY
GGLLGLLARLNPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPV
GATINMDGTAIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGL
VLTAAGLPLEGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDRAIYDSSNKE
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