GapMind for catabolism of small carbon sources

 

Protein WP_038023692.1 in Tatumella morbirosei LMG 23360

Annotation: NCBI__GCF_000757425.2:WP_038023692.1

Length: 328 amino acids

Source: GCF_000757425.2 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araH hi L-arabinose ABC transporter, permease protein AraH (characterized) 83% 98% 538.5 RbsC, 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) 38% 210.7
D-galactose catabolism BPHYT_RS16925 med Arabinose ABC transporter permease (characterized, see rationale) 59% 100% 374.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 34% 99% 215.3 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 98% 199.1 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-ribose catabolism rbsC lo ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 37% 95% 195.3 L-arabinose ABC transporter, permease protein AraH 83% 538.5
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 98% 162.5 L-arabinose ABC transporter, permease protein AraH 83% 538.5
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 33% 98% 162.5 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-cellobiose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-glucose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
lactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-maltose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 33% 91% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
sucrose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
trehalose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 32% 95% 161.8 L-arabinose ABC transporter, permease protein AraH 83% 538.5
D-xylose catabolism xylH lo D-xylose ABC transporter, permease protein (characterized) 36% 63% 141.4 L-arabinose ABC transporter, permease protein AraH 83% 538.5
2'-deoxyinosine catabolism H281DRAFT_01115 lo deoxynucleoside transporter, permease component 1 (characterized) 30% 81% 129.4 L-arabinose ABC transporter, permease protein AraH 83% 538.5

Sequence Analysis Tools

View WP_038023692.1 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

MTNSTSTPSATAPLAVSSGQRLNRLWNNFGMLVVFALLFIVCAIFVPNFATFINMKGLGL
AMSMSGMVACGMLFCLASGDFDLSVASVIACAGVVTAVVMNLTENMWIGVGAGLLLGCLT
GLVNGFVIARLKINALITTLATMQIVRGLAYIISDGKAVGIDDDSFFSLGYANWLGVPAP
IWLTILTMVVFGFLLNKTIFGRNTLAIGGNEEAARLAGVPVVRTRIIIFILSGLVSAAAG
IILASRMTSGQPMTSLGYELVVISACVLGGVSLKGGVGRISYVVAGVLILGTVENAMNLL
NISPFSQYVVRGAILLAAVIFDRYKQKS

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