GapMind for catabolism of small carbon sources

 

Finding step gtsD for D-glucose catabolism in Marinobacter adhaerens HP15

5 candidates for gtsD: glucose ABC transporter, ATPase component (GtsD)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi HP15_2955 ATP-binding component of ABC transporter ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 62% 95% 435.3 MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins 50% 361.3
med HP15_4062 spermidine/putrescine ABC transporter, ATP-binding protein Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 41% 88% 251.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 61% 426.0
med HP15_1347 sulfate/thiosulfate transporter subunit Sugar ABC transporter ATP-binding protein (characterized, see rationale) 42% 81% 228.4 CysA aka B2422, component of Sulfate/thiosulfate porter 59% 379.0
med HP15_939 spermidine/putrescine ABC transporter ATPase subunit ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
lo HP15_4067 spermidine/putrescine ABC transporter ATPase subunit Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.

Also see fitness data for the candidates

Definition of step gtsD

Or cluster all characterized gtsD proteins

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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