GapMind for catabolism of small carbon sources

 

Protein WP_012468795.1 in Trichlorobacter lovleyi SZ

Annotation: NCBI__GCF_000020385.1:WP_012468795.1

Length: 363 amino acids

Source: GCF_000020385.1 in NCBI

Candidate for 76 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 54% 100% 274.2 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 53% 268.9
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) 53% 97% 268.9 Arginine transport ATP-binding protein ArtM 54% 274.2
L-glutamate catabolism gltL 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) 53% 97% 268.9 Arginine transport ATP-binding protein ArtM 54% 274.2
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 97% 266.9 Arginine transport ATP-binding protein ArtM 54% 274.2
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 97% 266.9 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 54% 97% 257.3 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
L-histidine 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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 52% 93% 255.4 Arginine transport ATP-binding protein ArtM 54% 274.2
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 90% 254.6 Arginine transport ATP-binding protein ArtM 54% 274.2
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 90% 254.6 Arginine transport ATP-binding protein ArtM 54% 274.2
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 53% 99% 252.3 Arginine transport ATP-binding protein ArtM 54% 274.2
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 53% 99% 252.3 Arginine transport ATP-binding protein ArtM 54% 274.2
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 50% 97% 250 Arginine transport ATP-binding protein ArtM 54% 274.2
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 52% 94% 249.6 Arginine transport ATP-binding protein ArtM 54% 274.2
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 51% 94% 243.8 Arginine transport ATP-binding protein ArtM 54% 274.2
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% 91% 240.7 Arginine transport ATP-binding protein ArtM 54% 274.2
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 49% 95% 235.7 Arginine transport ATP-binding protein ArtM 54% 274.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 52% 92% 235 Arginine transport ATP-binding protein ArtM 54% 274.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 52% 92% 235 Arginine transport ATP-binding protein ArtM 54% 274.2
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 49% 99% 231.9 Arginine transport ATP-binding protein ArtM 54% 274.2
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 49% 99% 231.9 Arginine transport ATP-binding protein ArtM 54% 274.2
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 43% 72% 187.2 Arginine transport ATP-binding protein ArtM 54% 274.2
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 80% 155.2 Arginine transport ATP-binding protein ArtM 54% 274.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 41% 59% 183.3 Arginine transport ATP-binding protein ArtM 54% 274.2
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 37% 66% 171.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 64% 161.4 Arginine transport ATP-binding protein ArtM 54% 274.2
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 64% 161.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 66% 160.2 Arginine transport ATP-binding protein ArtM 54% 274.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 84% 159.8 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 38% 85% 159.1 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 67% 158.7 Arginine transport ATP-binding protein ArtM 54% 274.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 64% 156.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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) 33% 80% 156.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 63% 151 Arginine transport ATP-binding protein ArtM 54% 274.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 63% 151 Arginine transport ATP-binding protein ArtM 54% 274.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 63% 151 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 35% 63% 150.6 Arginine transport ATP-binding protein ArtM 54% 274.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 62% 150.6 Arginine transport ATP-binding protein ArtM 54% 274.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 70% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 35% 70% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 30% 78% 149.8 Arginine transport ATP-binding protein ArtM 54% 274.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 62% 149.1 Arginine transport ATP-binding protein ArtM 54% 274.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 34% 65% 148.3 Arginine transport ATP-binding protein ArtM 54% 274.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 61% 147.1 Arginine transport ATP-binding protein ArtM 54% 274.2
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 33% 63% 147.1 Arginine transport ATP-binding protein ArtM 54% 274.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 81% 146.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-cellobiose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-glucose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
lactose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
sucrose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
trehalose catabolism gtsD 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% 63% 141.4 Arginine transport ATP-binding protein ArtM 54% 274.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 139.4 Arginine transport ATP-binding protein ArtM 54% 274.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 139.4 Arginine transport ATP-binding protein ArtM 54% 274.2
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 139.4 Arginine transport ATP-binding protein ArtM 54% 274.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 62% 136.7 Arginine transport ATP-binding protein ArtM 54% 274.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 57% 135.2 Arginine transport ATP-binding protein ArtM 54% 274.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 66% 129.8 Arginine transport ATP-binding protein ArtM 54% 274.2
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 32% 95% 121.3 Arginine transport ATP-binding protein ArtM 54% 274.2

Sequence Analysis Tools

View WP_012468795.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIRVAHLSKTYGEVTVLKDISLSVAKGEVISIIGPSGTGKSTFLRCLNLLEQPSGGSIAV
DGIDLLDKKSDIPRIRQRMNMVFQSFNLFSHLTALENLTIGPVRLLGINKQEAEQKALEI
LKLVGLAEKADSFPDELSGGQKQRVAIARCLAMNPEIILFDEPTSALDPTMVSEVLAVIR
RLAKDGMTMLIVTHEMDFARDVSSRVLYMDEGLIYEEGTPQQIFENPQKEKTRAFINRIR
SFNYCISSADYDLYAMNAEIEIFCERQILPRKTRHNLLLLVEELLQIHTPLLATTALDLT
IAYSEKKESLEIILENRGEAVNLLDKDRLPDELGLNIITHLAQQIDYQRCEEINRVTVTL
KQG

This GapMind analysis is from Apr 09 2024. 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