GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0960 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0960 ATPase

Length: 417 amino acids

Source: SynE in FitnessBrowser

Candidate for 46 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism thuK 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) 48% 97% 329.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 48% 332.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
sucrose catabolism thuK 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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 48% 97% 329.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
trehalose catabolism thuK 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) 48% 97% 329.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 48% 332.8
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) 46% 99% 323.9 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 46% 96% 306.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 100% 302 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 100% 302 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 100% 302 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 100% 300.1 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 46% 98% 296.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 90% 296.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 43% 99% 295.8 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 46% 90% 293.9 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 42% 99% 292.4 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 99% 291.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 44% 98% 290 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 86% 283.5 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 97% 279.3 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 95% 273.5 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 52% 73% 272.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 41% 96% 264.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 49% 72% 256.1 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 49% 72% 256.1 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 43% 95% 255 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 43% 91% 254.6 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 71% 220.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 38% 99% 253.8 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 38% 99% 253.8 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 50% 67% 218.4 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 36% 90% 210.7 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 33% 91% 189.1 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 82% 167.2 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 42% 68% 166.4 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8
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) 35% 65% 162.5 Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 50% 337.8

Sequence Analysis Tools

View Synpcc7942_0960 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

LPRSAARVTSAKLFPTFGRDCNVAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADG
EFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPH
LSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDT
LLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGV
TTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVT
VRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGAAASKNLLITVTGVEA
LGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAIRPS

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 paper from 2022 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