GapMind for catabolism of small carbon sources

 

Protein CA265_RS15880 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS15880 sugar ABC transporter ATP-binding protein

Length: 330 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 57 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 86% 169.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 70% 157.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 70% 157.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 70% 157.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 70% 157.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 61% 156.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 61% 156.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 59% 154.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 31% 63% 153.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 71% 150.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 33% 62% 149.8 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism malK1 lo 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 (characterized) 33% 63% 149.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 34% 63% 148.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 65% 148.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 34% 64% 147.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 34% 64% 147.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 31% 90% 146.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 32% 62% 144.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 31% 77% 144.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 80% 142.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 80% 142.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 31% 62% 141.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 58% 140.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-cellobiose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-glucose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
lactose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism gtsD 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) 34% 58% 140.2 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 73% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 73% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 31% 79% 138.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 61% 138.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 32% 65% 138.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 63% 138.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 66% 137.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 66% 137.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 32% 66% 137.9 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 61% 137.1 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 30% 64% 134.4 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 96% 130.6 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
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) 31% 68% 128.3 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 61% 124 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 30% 87% 121.7 Fe(3+)-transporting ATPase; EC 3.6.3.30 31% 171.4

Sequence Analysis Tools

View CA265_RS15880 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSNTIISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTD
EGEIFFEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKAEKT
LQIMEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRA
DIKRVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQIL
GNAVVLSQADAEKIGLKTERNSVVFYPEWAEISNSWSSRRFEVKDVYYKGFYDELLLERN
GVSIRAIQLNRGAHKKNDYVQLNISRFLAF

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, 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