GapMind for catabolism of small carbon sources

 

Protein 3609758 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3141 ABC transporter related (RefSeq)

Length: 352 amino acids

Source: Dino in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 100% 349 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 100% 349 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism malK1 med 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) 51% 99% 347.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 50% 96% 335.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism malK_Sm med 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) 47% 100% 322 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
trehalose catabolism malK med 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) 47% 100% 322 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-cellobiose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-glucose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
lactose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-mannose catabolism TT_C0211 med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
sucrose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
trehalose catabolism gtsD med 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) 59% 72% 315.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 51% 89% 312 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 48% 95% 311.6 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-cellobiose catabolism msiK med 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) 56% 77% 307 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 95% 298.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 47% 100% 295 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 90% 285.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 87% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 77% 208.4 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 77% 208.4 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 77% 208.4 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 77% 208.4 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 42% 57% 183 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 51% 354.0

Sequence Analysis Tools

View 3609758 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

MAEVILKDLTKRWGDFVGVDNQSLHVRDEEFLVLLGPSGCGKTTTMRMIAGLEDPTDGEI
WIGDRMVNDDLPKDRDVAMVFQNYGLYPHMTIFENIAYPLRVRGVDKAEIPPRVQRAAEQ
VELTKFLHRKPKALSGGQRQRVALARAIVRKPKVFLMDEPLSNLDAKLRVTMRAELKHLS
RELQITTVYVTHDQIEAMTLADRVAVMKHGVIQQLGTPDEIYNDPANLFVAGFIGSPAMN
LINGSVEDGMFVTTGGTRLVKVPSPDRARAILGVRADDMQVHEAGQGDIDVTIYAFENTG
ESTLLTVQWGKQRVIARGDRHLRKEQDDVVGISLNTDHLYLFDPDTEERIRM

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