Finding step gltP for L-glutamate catabolism in Jannaschia aquimarina GSW-M26
No candidates for gltP: L-glutamate:cation symporter GltP/GltT
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step gltP
- Curated sequence P21345: Proton/glutamate-aspartate symporter; Glutamate-aspartate carrier protein; Proton-glutamate-aspartate transport protein. Glutamate/aspartate:H+ symporter, GltP or GltT; has 8 TMSs with 2 re-entrant loops as for GltPh (TC# 2.A.23.1.5). glutamate/aspartate : H+ symporter GltP
- Curated sequence P39817: Proton/glutamate-aspartate symporter; Proton/glutamate symport protein
- Curated sequence CH_088342: proton/sodium-glutamate symport protein GltT. Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein
- Curated sequence P24943: Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein. proton/sodium-glutamate symport protein GltT. Glutamate/aspartate:Na+ + H+ symporter
- UniProt sequence A1S570: SubName: Full=Sodium:dicarboxylate symporter {ECO:0000313|EMBL:ABL99526.1};
- UniProt sequence L0GT47: SubName: Full=Na+/H+ dicarboxylate symporter {ECO:0000313|EMBL:AGA88545.1};
- Ignore hits to O59010 when looking for 'other' hits (Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter. Archaeal aspartate transporter, Gltph (GltPh) (3-D structure known; 3V8F and 3V8G) (Boudker et al., 2007; Yernool et al., 2004). Cotransports aspartate with 2 Na+ (Ryan et al., 2009) or 3 Na+ (Groeneveld and Slotboom, 2010) or 1Na+ plus 1 H+ plus 1 K+)
Or cluster all characterized gltP proteins
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