GapMind for catabolism of small carbon sources


Finding step thuK for sucrose catabolism in Sphingomonas koreensis DSMZ 15582

5 candidates for thuK: sucrose ABC transporter, ATPase component ThuK

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
lo Ga0059261_3668 ABC transporter ABC transporter (characterized, see rationale) 38% 52% 124 ABC-type molybdate transporter (EC 46% 169.1
lo Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 62% 119.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
lo Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1) ABC transporter (characterized, see rationale) 31% 61% 117.5 phosphate ABC transporter, ATP-binding protein; EC 59% 312.8
lo Ga0059261_2412 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 65% 116.7 ATM1-type heavy metal exporter; ATP-binding cassette transporter Atm1; NaAtm1 62% 718.0
lo Ga0059261_1321 ABC-type antimicrobial peptide transport system, ATPase component 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) 31% 57% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 51% 216.5

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 thuK

Or cluster all characterized thuK proteins

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

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