GapMind for catabolism of small carbon sources

 

Protein Ga0059261_2293 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_2293 cell division ATP-binding protein FtsE

Length: 235 amino acids

Source: Korea in FitnessBrowser

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 63% 147.5 cell division ATP-binding protein ftsE 44% 185.3
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 33% 93% 132.1 cell division ATP-binding protein ftsE 44% 185.3
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 89% 129 cell division ATP-binding protein ftsE 44% 185.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 56% 127.1 cell division ATP-binding protein ftsE 44% 185.3
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 32% 90% 122.5 cell division ATP-binding protein ftsE 44% 185.3
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 32% 90% 122.5 cell division ATP-binding protein ftsE 44% 185.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 34% 57% 122.5 cell division ATP-binding protein ftsE 44% 185.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 62% 122.1 cell division ATP-binding protein ftsE 44% 185.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 62% 122.1 cell division ATP-binding protein ftsE 44% 185.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 62% 122.1 cell division ATP-binding protein ftsE 44% 185.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 62% 122.1 cell division ATP-binding protein ftsE 44% 185.3
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 35% 53% 120.2 cell division ATP-binding protein ftsE 44% 185.3
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 34% 56% 115.9 cell division ATP-binding protein ftsE 44% 185.3
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 34% 51% 115.2 cell division ATP-binding protein ftsE 44% 185.3
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 32% 51% 112.1 cell division ATP-binding protein ftsE 44% 185.3
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 51% 110.5 cell division ATP-binding protein ftsE 44% 185.3
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 51% 107.1 cell division ATP-binding protein ftsE 44% 185.3
D-mannose catabolism TT_C0211 lo 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% 51% 107.1 cell division ATP-binding protein ftsE 44% 185.3
trehalose catabolism thuK lo 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% 51% 107.1 cell division ATP-binding protein ftsE 44% 185.3
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 65% 90.9 cell division ATP-binding protein ftsE 44% 185.3

Sequence Analysis Tools

View Ga0059261_2293 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MANIVQFENVGLRYGTGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRG
IVRLFGEDAGALPRKRLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGP
VREMIAWVGLKDRDSAKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLL
HLFDSLNRLGTTVVVATHDFQLISRIPDARMMRIEKGRLNDPTGALRYPPGQAPA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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