GapMind for catabolism of small carbon sources

 

Protein WP_094932427.1 in Nocardiopsis gilva YIM 90087

Annotation: NCBI__GCF_002263495.1:WP_094932427.1

Length: 414 amino acids

Source: GCF_002263495.1 in NCBI

Candidate for 57 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuK hi Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 53% 98% 377.9 Diacetylchitobiose uptake system ATP-binding protein MsiK; EC 7.5.2.- 51% 359.4
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 55% 95% 361.7 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 49% 99% 350.5 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 99% 348.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 53% 91% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 54% 88% 342.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 50% 98% 339.7 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 51% 92% 330.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
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) 51% 92% 330.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 52% 90% 326.2 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 50% 100% 324.3 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 47% 97% 310.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 91% 308.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 91% 308.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 51% 91% 308.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 49% 96% 308.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 51% 92% 305.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 98% 305.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 45% 99% 303.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 49% 87% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 301.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 51% 87% 300.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 50% 79% 299.7 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 99% 295.4 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 48% 88% 287.3 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 56% 72% 283.5 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 57% 74% 280.4 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 57% 74% 280.4 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 48% 84% 274.6 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 43% 79% 250.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 47% 87% 241.1 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 91% 211.8 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 204.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 204.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 204.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 94% 204.9 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 36% 92% 188.7 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 82% 179.5 Trehalose import ATP-binding protein SugC; EC 7.5.2.- 53% 377.9

Sequence Analysis Tools

View WP_094932427.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MARVQLAGVGKTYPDGTSAVSGLDLDIGEGEFLVLVGPSGCGKSTALRMIAGLEEITAGT
LSIGDRVVNRTPARDRDVAMVFQSYALYPHLSVRDNIGFGLQLRKLPKAEIKERVEEAAA
TLGLTEHLDRRPRNLSGGQRQRVAMGRAIVRSPKAFLMDEPLSNLDAKLRVQMRAEISRI
QRNLGVTTIYVTHDQVEAMTLGDRVAVLKKGVLQQVAPPQELYERPANIFVAGFIGSPAM
NLLQARLETDAPTDAGARLVVGGQTLDVPAATVDERGLGAYVGRDIAVGIRPEDMDDADL
SPEADGSVLTSTTELVEALGSELLVHFRLDAPPVVTEDTRELARDVGVDVDAGDAGGTES
DITARFSPRSSTAIGRPVRVRVDTARLYFFDPATGAGIWGDPASHSSEVEGTHA

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