Protein WP_038016164.1 in Tatumella morbirosei LMG 23360
Annotation: NCBI__GCF_000757425.2:WP_038016164.1
Length: 291 amino acids
Source: GCF_000757425.2 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 |
|---|
| D-ribose catabolism | rbsB | hi | D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized) | 81% | 99% | 463.4 | RbsB, 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) | 73% | 417.9 |
| myo-inositol catabolism | ibpA | lo | Inositol ABC transporter, periplasmic inositol-binding protein IbpA, 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) | 33% | 94% | 160.2 | D-ribose-binding periplasmic protein; EC 3.6.3.17 | 81% | 463.4 |
| myo-inositol catabolism | PS417_11885 | lo | Inositol transport system sugar-binding protein (characterized) | 31% | 96% | 149.8 | D-ribose-binding periplasmic protein; EC 3.6.3.17 | 81% | 463.4 |
| D-fructose catabolism | fruE | lo | Fructose import binding protein FruE (characterized) | 31% | 93% | 123.2 | D-ribose-binding periplasmic protein; EC 3.6.3.17 | 81% | 463.4 |
| sucrose catabolism | fruE | lo | Fructose import binding protein FruE (characterized) | 31% | 93% | 123.2 | D-ribose-binding periplasmic protein; EC 3.6.3.17 | 81% | 463.4 |
| D-xylose catabolism | xylE_Tm | lo | Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale) | 31% | 79% | 99 | D-ribose-binding periplasmic protein; EC 3.6.3.17 | 81% | 463.4 |
Sequence Analysis Tools
View WP_038016164.1 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
MKKLTALALLLGATLSTQALAKDTIALVISTLDNPFFVSLKDGAQKEADKLGYNLVVLDS
QNNPAKELANVQDLMVRGTKAILINPTDSDAVGNSVKIANQAHIPVITLDRAASQGKVVS
HIASDNVAGGKMAGDFIAKQLGDGAKVIELEGIAGTSVARERGEGFKQASDAHKFDIIAS
QPADFDRTKGLNVMQNLLTAHPDVQAVFAQNDEMALGAMRALQTAGKSGVLVVGFDGTPD
GVKAVQSGKLAATVAQLPEKIGEIGVDTADKVLKGQQVEARIPVDLKLITK
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