Protein WP_086005351.1 in Rhizobium freirei PRF 81
Annotation: NCBI__GCF_000359745.1:WP_086005351.1
Length: 477 amino acids
Source: GCF_000359745.1 in NCBI
Candidate for 8 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| myo-inositol catabolism | PS417_11890 | med | m-Inositol ABC transporter, ATPase component (itaA) (characterized) | 46% | 91% | 401.4 | Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 45% | 399.8 |
| D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 43% | 91% | 393.7 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| D-xylose catabolism | xylK_Tm | med | Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) | 45% | 92% | 393.3 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| D-galactose catabolism | BPHYT_RS16930 | med | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 45% | 90% | 380.9 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| myo-inositol catabolism | iatA | med | Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) | 42% | 93% | 374.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| D-fructose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 90% | 359.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| sucrose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 90% | 359.8 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
| D-galactose catabolism | ytfR | med | galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) | 40% | 95% | 352.4 | m-Inositol ABC transporter, ATPase component (itaA) | 46% | 401.4 |
Sequence Analysis Tools
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MNLKVRRGRVHTLLGENGAGKSTLMKILAGVYKPTSGEILLAGKAYQPQNPRDARGHGIS
IVFQELSLCRNLSVAQNIFASHEPSRFGFVRDRVLVAKAEALIEDLGLPVNVHAKVGDLS
IAQRQLVEIAKGLSLPADVIILDEPTSSLSDSEAEILFSIIERLKARGKAIIYISHRMEE
IMRLSDDITVIRDGEYVTTTEKSETSIDKLIALMVGREMQDIYPPRVAPRPAESTAPVLA
TKNLTVPGKFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGMERPEGQIFLDGKPLTLA
SPSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRGSAERAAAKAEV
LRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDVGAKFEIYRIIR
ELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPETVMTYAAGMHA
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