Protein WP_067073554.1 in Methanoculleus horonobensis T10
Annotation: NCBI__GCF_001602375.1:WP_067073554.1
Length: 431 amino acids
Source: GCF_001602375.1 in NCBI
Candidate for 4 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-tryptophan catabolism | tnaT | lo | High affinity tryptophan:Na+ symporter, TnaT, of 501 aas and 12 TMSs (Androutsellis-Theotokis et al., 2003). The Km for Tryptophan is 145 nM; tryptamine and serotonin weakly inhibited with Ki values of 200 and 440 μM, respectively. An evolutionarily conserved role of adjacent transmembrane segments 7 and 8 has been proposed (characterized) | 33% | 90% | 254.6 | Neurotransmitter:sodium symporter of 455 aas, MhsT | 40% | 319.3 |
| L-alanine catabolism | metP | lo | Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized) | 38% | 70% | 236.5 | Neurotransmitter:sodium symporter of 455 aas, MhsT | 40% | 319.3 |
| L-tyrosine catabolism | tyt1 | lo | The 11 TMS Na+-dependent tyrosine transporter, Tyt1 (characterized) | 30% | 99% | 193.7 | Neurotransmitter:sodium symporter of 455 aas, MhsT | 40% | 319.3 |
| L-leucine catabolism | leuT | lo | The amino acid (leucine):2 Na+ symporter, LeuTAa (Yamashita et al., 2005). LeuT possesses two ion binding sites, NA1 and NA2, both highly specific for Na+ but with differing mechanisms of binding (Noskov and Roux, 2008). X-ray structures have been determined for LeuT in substrate-free outward-open and apo inward-open states (characterized) | 36% | 58% | 164.9 | Neurotransmitter:sodium symporter of 455 aas, MhsT | 40% | 319.3 |
Sequence Analysis Tools
View WP_067073554.1 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
MAREHWSSTLGFILASIGSAVGIGNIWRFPYIVGANGGGAFLIPFLIAVLLFGLPLMVLE
LAIGRSTGTSVISAFRSIRQRFAAAGLVIVAVISLILGYYLVITSWVLAYAIFFAFNRPM
EFDAFTGSYLPLVFFLLSGLAVYVTVRSGVRSGIERASRYLIPALFVILIFLVVFSLTEP
GAAEGIGFYLSPDFSRLADPGVWIAAFGQAFFSLSVGMGILLTFGSYLGREALFRNAAII
AAADMLIAVLAGLVIFPLVFTAGLDPAAGVNLAFITLPAAFTEIQYGMVLGALFFLMLFA
AALTSAVSMLEVPTAALMDSYGLPRKRATLLVFAAVMLLGLPSALSYTALNLEALGMPFL
DLADYVFGTIGLIVAGLIVSIVGGWFMTRTRICAEIGGCGWQQTVYMALIRYGVPAVLLI
TLVGSFFQGAG
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