GapMind for catabolism of small carbon sources

 

Protein WP_014264772.1 in Granulicella mallensis MP5ACTX8

Annotation: NCBI__GCF_000178955.2:WP_014264772.1

Length: 248 amino acids

Source: GCF_000178955.2 in NCBI

Candidate for 60 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 43% 78% 172.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 88% 144.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 88% 144.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-glutamate catabolism gltL med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 88% 144.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 46% 55% 179.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
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) 40% 68% 174.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 42% 56% 167.9 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 73% 156.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
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) 39% 83% 156 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 60% 150.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 60% 150.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 85% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 85% 148.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 42% 59% 146 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 59% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 52% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 59% 144.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 56% 143.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 58% 143.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 58% 143.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 39% 58% 142.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-arginine catabolism artP lo Histidine transport ATP-binding protein HisP (characterized) 34% 93% 141.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 93% 141.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 93% 141.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 57% 140.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 55% 140.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 53% 139.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 89% 139 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 37% 61% 138.3 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 81% 137.5 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-asparagine catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-aspartate catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-glutamate catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-histidine catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-leucine catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
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) 40% 52% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-proline catabolism aapP lo 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) 37% 88% 137.1 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
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) 38% 58% 136.7 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
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) 36% 87% 135.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 86% 135.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 86% 135.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 52% 134.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 55% 134.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 81% 131 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 60% 131 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 60% 130.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-citrulline catabolism PS417_17605 lo 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) 37% 78% 130.2 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 31% 83% 124 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 31% 67% 119.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 60% 118.6 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 100% 114.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 100% 114.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 100% 114.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 74% 114.4 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 68% 109.8 Glycine betaine/carnitine/choline transport ATP-binding protein OpuCA 44% 208.4

Sequence Analysis Tools

View WP_014264772.1 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

MATQDVEFAQVSFTVEGGRQLLSEISLRVEPGTTTALLGRSGSGKTTLLRTVNALVRPTS
GRVLVGGQDVSKTDVIALRRGIGYVIQESGLFPHMSIERNVGMALELSGKPKAEIAARAA
EMLHLVGLPEEMAKRYPWQLSGGQRQRVGLARALASNPEVLLMDEPFGALDPLTRAEMQT
MLRDLLRRVGKTTFIVTHDLEEALYLAGRVVLLEAGRIVANLAADEVRGSQNEAMRAYVA
ATHRGEAA

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