GapMind for catabolism of small carbon sources

 

Protein WP_025761286.1 in Dyadobacter tibetensis Y620-1

Annotation: NCBI__GCF_000566685.1:WP_025761286.1

Length: 252 amino acids

Source: GCF_000566685.1 in NCBI

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 69% 156.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 96% 153.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
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) 34% 95% 149.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-glutamate catabolism gltL 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) 34% 95% 149.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 147.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 91% 147.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 91% 147.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 147.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 97% 147.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-histidine catabolism hisP lo 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) 34% 96% 147.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 35% 69% 146.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 97% 146 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 97% 146 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 87% 142.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 62% 140.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 65% 139.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 65% 139.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 65% 139.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 33% 66% 137.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 58% 134.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
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) 31% 88% 133.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 64% 132.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 61% 123.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 122.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 122.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 122.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) 30% 98% 122.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
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) 32% 75% 119 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 33% 79% 114 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 30% 69% 96.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 39% 172.2

Sequence Analysis Tools

View WP_025761286.1 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

MENSSKEPIIKISDLYKSFGDLDVLKGVNLNVYRGENVVVLGRSGTGKSVLIKILVGLLT
QDSGIANVLGREVSELNESELRDLRLKIGFSFQNSALYDSMTVRENLEFPLVRNVPNLTR
AEIDEAVETVLEAVGLLQTINQVPSELSGGQRKRIGIARTLILKPEIMLYDEPTAGLDPI
TCLEINELINEVKEKYKTTAIIITHDLTCAKATGDRIAMLLDGIFVRQGTFEEVFKTEEE
RIKSFYDYNFIQ

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