GapMind for catabolism of small carbon sources

 

Protein WP_035589370.1 in Hippea jasoniae Mar08-272r

Annotation: NCBI__GCF_000744435.1:WP_035589370.1

Length: 241 amino acids

Source: GCF_000744435.1 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-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 59% 99% 279.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 58% 100% 277.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 55% 97% 274.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 86% 268.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 86% 268.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 264.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 264.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 54% 100% 264.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 54% 100% 264.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 56% 87% 264.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 56% 88% 262.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 56% 88% 262.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 56% 88% 262.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 56% 88% 262.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 56% 88% 262.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 55% 89% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 51% 92% 250.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 51% 96% 246.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 48% 94% 241.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism hisP med Histidine transport ATP-binding protein HisP (characterized) 53% 95% 239.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 49% 94% 238.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 49% 98% 238 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 48% 99% 229.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 48% 99% 229.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 47% 90% 214.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-tryptophan catabolism ecfA1 med Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 40% 76% 133.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 73% 180.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 41% 60% 175.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 42% 58% 171.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 39% 64% 162.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
trehalose catabolism thuK 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) 39% 64% 162.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 39% 82% 158.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 39% 82% 158.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 61% 153.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 68% 148.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 68% 148.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 69% 147.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 63% 146 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 37% 59% 143.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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% 64% 142.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 36% 67% 139.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 34% 64% 139.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 67% 138.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 60% 138.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 35% 60% 137.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 60% 137.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 60% 137.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 61% 135.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 64% 134.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 60% 134 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
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) 34% 95% 132.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 55% 132.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 77% 129.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 60% 111.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 87% 111.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 58% 283.9

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Sequence

MIVAEHLHKTFPNGVKALRDVSLNVKKGEVVVIIGASGSGKTTFLRTINQLETVDEGKII
VEGIDITDPKTNLTKIRADIGMVFQHFNVFPHLTVLENVMIGQILVRKRKKEEAKKIAID
FLTKVGIADKKDDYPTNLSGGQQQRVAIARALAMNPKIMLFDEATSALDPEMVGGILDIM
KQLAREGITMVVVTHEMGFAKEAADRIVYMDSGKIVEMGTPEEIFNNPKSDRLKQFLSQI
L

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