GapMind for catabolism of small carbon sources

 

Protein WP_049771236.1 in Sphingomonas wittichii RW1

Annotation: NCBI__GCF_000016765.1:WP_049771236.1

Length: 238 amino acids

Source: GCF_000016765.1 in NCBI

Candidate for 81 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 64% 94% 308.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 63% 307.4
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 63% 92% 307.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 63% 93% 305.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 63% 93% 305.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 63% 93% 305.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 63% 93% 305.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 63% 93% 305.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 291.2 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 291.2 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 62% 90% 291.2 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 64% 90% 289.3 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 64% 90% 289.3 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 58% 92% 285.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 55% 98% 260.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 55% 98% 260.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 52% 98% 250 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 52% 98% 236.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 52% 98% 236.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-asparagine catabolism glnQ med 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) 50% 94% 231.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 49% 93% 230.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 50% 94% 228 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 49% 96% 226.1 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 93% 225.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 50% 93% 225.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 51% 89% 223.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 45% 67% 176.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 64% 157.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 67% 156.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 65% 152.1 ABC transporter for D-Alanine, ATPase component 64% 308.9
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 65% 152.1 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 69% 151.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 61% 150.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 39% 60% 150.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 66% 149.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 56% 148.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 64% 147.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 62% 147.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 64% 147.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 82% 146.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 66% 146 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 60% 144.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 37% 61% 144.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 77% 144.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 37% 57% 144.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 60% 142.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 54% 142.1 ABC transporter for D-Alanine, ATPase component 64% 308.9
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) 35% 59% 140.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 82% 139.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 62% 138.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 58% 137.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
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) 34% 60% 136 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 58% 134.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 58% 134.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 58% 134.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 58% 134.8 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 60% 134.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
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% 61% 132.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
trehalose catabolism malK 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% 61% 132.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
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) 33% 58% 129 ABC transporter for D-Alanine, ATPase component 64% 308.9
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 68% 128.3 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 89% 119 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 36% 89% 117.9 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 73% 115.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 35% 84% 110.5 ABC transporter for D-Alanine, ATPase component 64% 308.9
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 63% 109.4 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 108.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 108.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 108.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 108.6 ABC transporter for D-Alanine, ATPase component 64% 308.9
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 62% 101.7 ABC transporter for D-Alanine, ATPase component 64% 308.9
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 85% 99.8 ABC transporter for D-Alanine, ATPase component 64% 308.9

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Sequence

MAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGED
EVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLER
VRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALA
TEGITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSRLLY

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