Protein YP_001328980.1 in Sinorhizobium medicae WSM419
Annotation: NCBI__GCF_000017145.1:YP_001328980.1
Length: 359 amino acids
Source: GCF_000017145.1 in NCBI
Candidate for 16 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannitol catabolism | mtlK | hi | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 57% | 98% | 400.6 | ABC transporter for Lactose, ATPase component | 58% | 390.6 |
| D-sorbitol (glucitol) catabolism | mtlK | hi | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 57% | 98% | 400.6 | ABC transporter for Lactose, ATPase component | 58% | 390.6 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 58% | 99% | 390.6 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 56% | 99% | 382.5 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 56% | 99% | 382.5 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 56% | 99% | 382.5 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 56% | 99% | 382.5 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-maltose catabolism | malK | med | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 56% | 97% | 380.2 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 53% | 95% | 337.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 47% | 97% | 317.8 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 33% | 97% | 198.4 | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK | 57% | 400.6 |
Sequence Analysis Tools
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
MATSVVLQKVEKRYGAFDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEITGGT
LLLDSDRMNEVAPAKRGIAMVFQSYALYPHMSVYKNLAFGLETAGYRKAEIEPKVRRAAE
ILQIEKLLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRL
HRDLGNTMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKM
NFLKARIEEVGGNETAVQVCGGALRLPRRLEGATQGQEVTFGIRPEHLSAHEGGIALAQI
NVEIVENLGGETMLYGITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGSDGRAM
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