GapMind for catabolism of small carbon sources

 

Protein WP_008411021.1 in Desulfotomaculum hydrothermale Lam5

Annotation: NCBI__GCF_000315365.1:WP_008411021.1

Length: 311 amino acids

Source: GCF_000315365.1 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
D-ribose catabolism rbsB med D-ribose-binding periplasmic protein; EC 3.6.3.17 (characterized) 54% 99% 314.7 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) 57% 322.8
myo-inositol catabolism PS417_11885 lo Inositol transport system sugar-binding protein (characterized) 32% 97% 165.6 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) 57% 322.8
D-mannose catabolism HSERO_RS03635 lo ABC-type sugar transport system, periplasmic component protein (characterized, see rationale) 37% 94% 164.9 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) 57% 322.8
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% 88% 161.4 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) 57% 322.8
L-arabinose catabolism araUsh lo Periplasmic binding protein/LacI transcriptional regulator (characterized, see rationale) 34% 85% 147.9 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) 57% 322.8
xylitol catabolism PS417_12055 lo Putative xylitol transport system substrate-binding protein; SubName: Full=Sugar ABC transporter substrate-binding protein (characterized, see rationale) 33% 80% 137.9 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) 57% 322.8

Sequence Analysis Tools

View WP_008411021.1 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

MKKFWKLTAVLLSVVFLAGLVSGCAGKQQAQEAPKAEEQKQLTIGLALSTLNNPFFVDMK
DGAQAAADKIGAKLVVMDAQDDASKQVSQVEDLIQQKVDVILLNPTDSDGLVTAVKDANK
ANIPVITLDRSVNGGTVVSHIASDNVAGGKMAADFIVEQLKGKGKVVELEGIAGTSAARD
RGQGFHEVMDKQTDIKVVAKQPADFDRSKGMSVMENILQSQPEINAVFAHNDEMALGALQ
AIEAAKKQILVVGFDGNDDAVKAVNDGKMAATVAQQPKLIGELGVQVAEKVKKGEKVEAQ
IPAELKLITKQ

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:

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:

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:

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