GapMind for catabolism of small carbon sources

 

Protein SM_b20235 in Sinorhizobium meliloti 1021

Annotation: FitnessBrowser__Smeli:SM_b20235

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

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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:

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