GapMind for catabolism of small carbon sources

 

Protein SM_b20235 in Sinorhizobium meliloti 1021

Annotation: SM_b20235 sugar ABC transporter ATP-binding protein

Length: 363 amino acids

Source: Smeli in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism SM_b21106 hi ABC transporter for L-Fucose, ATPase component (characterized) 54% 100% 374.8 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 54% 357.1
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 51% 99% 359 ABC transporter for L-Fucose, ATPase component 54% 374.8
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) 54% 98% 357.1 ABC transporter for L-Fucose, ATPase component 54% 374.8
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) 53% 97% 350.9 ABC transporter for L-Fucose, ATPase component 54% 374.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 52% 97% 337.8 ABC transporter for L-Fucose, ATPase component 54% 374.8
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) 48% 100% 321.6 ABC transporter for L-Fucose, ATPase component 54% 374.8
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) 48% 100% 321.6 ABC transporter for L-Fucose, ATPase component 54% 374.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 90% 318.5 ABC transporter for L-Fucose, ATPase component 54% 374.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 40% 92% 254.6 ABC transporter for L-Fucose, ATPase component 54% 374.8
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 79% 213.4 ABC transporter for L-Fucose, ATPase component 54% 374.8
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 79% 213.4 ABC transporter for L-Fucose, ATPase component 54% 374.8
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 79% 213.4 ABC transporter for L-Fucose, ATPase component 54% 374.8
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 79% 213.4 ABC transporter for L-Fucose, ATPase component 54% 374.8

Sequence Analysis Tools

View SM_b20235 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

MASVEIRNVVKRFGALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDGAV
VIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAATM
LGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKGLH
QRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPSMN
FIEGEVVGGTFRAPGGIIIPAPDLAHKGPTVAGIRPNKLQIGATGPSAKVLIVEPTGDET
HLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVHFFDGQTTLRLGALPGEVRNGFPP
ASA

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