Protein WP_011428142.1 in Rhizobium etli CFN 42
Annotation: NCBI__GCF_000092045.1:WP_011428142.1
Length: 511 amino acids
Source: GCF_000092045.1 in NCBI
Candidate for 10 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-rhamnose catabolism | rhaT' | hi | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) | 91% | 100% | 907.9 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 45% | 438.3 |
| D-ribose catabolism | rbsA | med | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) | 45% | 98% | 438.3 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| myo-inositol catabolism | PS417_11890 | med | Inositol transport system ATP-binding protein (characterized) | 43% | 97% | 425.6 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| D-fructose catabolism | fruK | med | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 41% | 98% | 385.2 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| sucrose catabolism | fruK | med | Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) | 41% | 98% | 385.2 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| D-galactose catabolism | mglA | med | Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) | 40% | 97% | 383.6 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| L-arabinose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 40% | 98% | 375.2 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| D-galactose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 40% | 98% | 375.2 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| xylitol catabolism | PS417_12065 | med | D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 40% | 99% | 362.5 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
| 2'-deoxyinosine catabolism | H281DRAFT_01113 | lo | deoxynucleoside transporter, ATPase component (characterized) | 38% | 99% | 345.5 | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) | 91% | 907.9 |
Sequence Analysis Tools
View WP_011428142.1 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
MNAAFQQPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKS
TLVKILTGIYRPNEGEILVDGQPTSFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGH
APRTRLRTIDWQTMNSRSKTLLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVI
MDEPTAALSRKEIDDLFRIVRGLKDQGKAILFISHKFDELYEIADDFVVFRDGRAVGQGR
LKETPQDEIVRMMVGRDVENVFPKIDVAIGGPVLEVEKYCHRTEFRDVSLTLRRGEILGI
YGLIGAGRSELAQSLFGVTKPLSGRLTLEGREISINSPHDAIKAGIVYVPEERGRHGLAL
PMPIYQNMTLPSLARTSRKGFLKAAEEFALARKYAERLDLRAAALSVPVGTLSGGNQQKV
VIGKWLATMPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMISSELPEIIGMSDR
VLVMKEGLSVGLFERDQLSPEALVRAATGNA
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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