GapMind for catabolism of small carbon sources

 

Protein WP_067911580.1 in Novosphingobium fuchskuhlense FNE08-7

Annotation: NCBI__GCF_001519075.1:WP_067911580.1

Length: 262 amino acids

Source: GCF_001519075.1 in NCBI

Candidate for 68 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 40% 85% 156.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 66% 154.1 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 66% 154.1 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 56% 150.6 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 34% 72% 147.9 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 57% 146.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 60% 144.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 66% 144.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
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% 55% 143.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism thuK 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% 55% 143.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 36% 63% 142.9 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 35% 54% 142.5 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 64% 141.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 64% 141.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 59% 141.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 81% 139.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 59% 138.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 52% 138.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 60% 136.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 54% 136.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism malK lo 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) 34% 56% 135.6 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 57% 134.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
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) 34% 65% 132.5 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 53% 132.5 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 54% 129.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 53% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 53% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 58% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 58% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 53% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 37% 58% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 55% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 30% 74% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 53% 129.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 84% 129 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 59% 129 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
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) 35% 55% 129 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 87% 128.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 87% 128.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
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) 34% 60% 128.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 87% 128.3 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 33% 88% 125.9 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 58% 125.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 54% 124.4 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 67% 113.2 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 35% 88% 110.9 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 102.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 102.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 102.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 83% 102.8 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 84% 94.7 CynD, component of Bispecific cyanate/nitrite transporter 44% 169.5

Sequence Analysis Tools

View WP_067911580.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MSALLSLRNVWVEYGEKVVLEKVNLEVSEGAFLSIIGPSGAGKSSLLRLILGQEAPTRGQ
VLLGGEPLEPQCGPDRGVVFQRYSVFPHMSVLGNVMFGLECPAAPIAARLFGSARRKAMG
EAAAMLHAVGLGDSLNLYPAQMSGGMQQRLAIAQALIKRPRILLLDEPFGALDPGIRADM
HGLITQLWRDYGLTIVMVTHDIKEAFTLGTRVLALDKRRHDPHAPHRYGATAVYDLPLRT
APAVVPPAPPQPDPNPLSAAAS

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