Protein WP_004124104.1 in Rhizobium freirei PRF 81
Annotation: NCBI__GCF_000359745.1:WP_004124104.1
Length: 492 amino acids
Source: GCF_000359745.1 in NCBI
Candidate for 6 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| xylitol catabolism | PS417_12065 | hi | 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) | 53% | 99% | 483 | m-Inositol ABC transporter, ATPase component (itaA) | 47% | 443.4 |
| myo-inositol catabolism | PS417_11890 | hi | m-Inositol ABC transporter, ATPase component (itaA) (characterized) | 47% | 94% | 443.4 | RbsA, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 46% | 416.4 |
| D-ribose catabolism | rbsA | med | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) | 45% | 97% | 416 | m-Inositol ABC transporter, ATPase component (itaA) | 47% | 443.4 |
| L-rhamnose catabolism | rhaT' | med | 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) | 43% | 96% | 395.2 | m-Inositol ABC transporter, ATPase component (itaA) | 47% | 443.4 |
| L-fucose catabolism | HSERO_RS05250 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 44% | 94% | 394 | m-Inositol ABC transporter, ATPase component (itaA) | 47% | 443.4 |
| D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 42% | 95% | 387.1 | m-Inositol ABC transporter, ATPase component (itaA) | 47% | 443.4 |
Sequence Analysis Tools
View WP_004124104.1 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
MEFLLEVEGLKKSFGGVAALRDGCFQLRPGSVHALCGGNGAGKSTFLKILMGIHKRDAGS
IRRRGKDVDYASPAAALAAGIAIIEQELSPIPHMTVAENIYLGREPSARFGGIDFKTMNR
NAQALLDRLRFNIRATQFMMNLSVAQIQLVEIAKALSHDAEVIFMDEPTSAIGEKEAQQL
FSTIERLKAEGKGVVYVSHRLSEIFQIADSYTAFRDGSYVGSGALADIDRPGLIRMIVGR
ELGEEYIKTNVPTATPGLEVAGLTAEGKLNDISFTAHKGEIFGIYGLMGSGRTEIFNCIF
GLDVLNSGQIKLAGQPITVGKPAEAMQHGIAFVTEDRKLTGLNLIDSVRNNICLASLPEM
SPRFSMDSRAEASASQDMIERFGIKAARDSMPVSGLSGGNQQKVVLGKWFLRKPKVLLLD
EPTRGVDVGAKREIYRIICDFAAEGGTVIMISSEIDEVLGMSDRILVMRQGRSAGILKRE
EADAQSLVHLST
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