GapMind for catabolism of small carbon sources

 

Protein WP_075663378.1 in Corynebacterium frankenforstense ST18

Annotation: NCBI__GCF_001941485.1:WP_075663378.1

Length: 343 amino acids

Source: GCF_001941485.1 in NCBI

Candidate for 63 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 59% 93% 362.5 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 62% 82% 348.6 ABC-type maltose transporter (EC 7.5.2.1) 59% 362.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 53% 93% 318.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 51% 99% 317 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 99% 315.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 48% 99% 312 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 50% 95% 307 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
trehalose catabolism malK med MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 49% 92% 306.6 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 51% 94% 305.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 50% 99% 302.4 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 50% 94% 299.3 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 50% 94% 299.3 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 47% 100% 295.4 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 51% 84% 283.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 48% 97% 279.6 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 46% 99% 271.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 96% 270.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 91% 268.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 99% 266.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 46% 86% 263.5 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 43% 88% 238.4 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
putrescine catabolism potA med Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 40% 71% 202.2 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 41% 71% 138.7 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 61% 68% 315.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
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) 61% 67% 296.6 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 56% 63% 276.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 55% 63% 273.5 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 96% 189.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 98% 189.1 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 39% 73% 186.4 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 92% 182.6 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 72% 181.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 72% 181.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 72% 181.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 72% 181.8 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 56% 153.3 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 38% 86% 146.7 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 81% 145.2 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 80% 124.4 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 58% 370.5

Sequence Analysis Tools

View WP_075663378.1 at NCBI

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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

MAPVTYDNVTVRYPGADHPSVTDFNLEIADGEFLVLVGPSGCGKSTTLRALAGLEPVESG
RILIGDDDVTDSDPAARDVAMVFQNYALYPHLSVRKNMSFALDLRKVPRDEADTRVAEAA
EILGLTDFLDRKPKDLSGGQRQRVAMGRAIVRNPRVFLMDEPLSNLDAKLRVSTRSEIAA
LQRRLGVTTVYVTHDQVEAMTMGDRVAVLDRGVLQQVAPPRELYRDPVNLFVAGFIGSPS
MNLFHDDVPGAGDVTFGVRPEHMRLLGAGEACPAGFRELTGPVDIVEELGAESYVYAHRD
GGRLVARLLDAPAPERGAEVRMAYDPAAALRFGPDGSRADARD

This GapMind analysis is from Sep 24 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