GapMind for catabolism of small carbon sources

 

Protein 7026373 in Shewanella sp. ANA-3

Annotation: Shewana3_3515 ABC transporter related (RefSeq)

Length: 349 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 60 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 39% 86% 220.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 92% 206.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 96% 204.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 86% 199.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 97% 199.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 85% 197.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 34% 98% 196.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 36% 82% 194.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 43% 68% 194.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 43% 68% 194.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 82% 194.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 82% 194.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 77% 193.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 70% 193 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 32% 96% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 77% 191 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 78% 190.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 81% 187.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 83% 186.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 98% 186 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 98% 186 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 98% 186 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 65% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
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) 36% 80% 184.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
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) 39% 67% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 95% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 76% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
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) 35% 73% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 76% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 76% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 76% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 56% 176.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 77% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 61% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 76% 163.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 95% 157.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 85% 156.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 36% 95% 151.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 36% 99% 146 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 98% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 98% 139 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 73% 125.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 265.0

Sequence Analysis Tools

View 7026373 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

MTSTLNLHQVHSDYQGQQVLKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGE
IQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGVAKLTPAQRKARLDDM
LALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIR
SILKQRNVSAVFVTHSKDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSG
NYLPAEVIDGHSVVTPIGELRSLTPLSQSHAFNGQVFLRPQQLALSADDAGVGTITERRF
LGAFCHYWVKVEAASHAHYVEVRSQIMQLNVGQRVVLSTEPHALVLFES

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