GapMind for catabolism of small carbon sources

 

Protein WP_055444491.1 in Lacinutrix himadriensis E4-9a

Annotation: NCBI__GCF_001418105.1:WP_055444491.1

Length: 259 amino acids

Source: GCF_001418105.1 in NCBI

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 40% 92% 162.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
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) 40% 92% 162.2 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 97% 162.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 97% 162.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 90% 156 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-arginine catabolism artP 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) 35% 96% 146.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
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) 35% 96% 146.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-lysine 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) 35% 96% 146.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 82% 143.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 82% 143.3 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 33% 60% 142.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 84% 139.4 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 94% 137.5 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 57% 136.7 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 68% 134 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 68% 134 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 68% 134 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 62% 129.8 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 31% 57% 125.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 62% 124 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 62% 124 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 32% 81% 122.1 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 57% 120.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 57% 120.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 57% 120.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 31% 54% 120.6 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7
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) 32% 73% 117.9 Protein TRIGALACTOSYLDIACYLGLYCEROL 3, chloroplastic; ABC transporter I family member 13; ABC transporter ABCI.13; AtABCI13; Non-intrinsic ABC protein 11; AtNAP11 37% 168.7

Sequence Analysis Tools

View WP_055444491.1 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

Fitness BLAST: loading...

Sequence

MNTGQNNSKAIENIETKSVMLEIKDLRKSFGDNAVLNGFNLKLYEGENLVIMGKSGSGKS
VMIKCLVGLLQADSGSIKIMDQEINTLNQKDLNILRTEIGFLFQGSALYDSMTVRENLEF
PLRRHKTRFKDASNMDELVTEALESVGLLHTVDLMPAELSGGMKRRIALARTLILKPKII
LYDEPTSGLDPITSKEIIALMRSIQKQYKTSSLIITHDVDCARVVSERIVLLVDGVNYVE
GTYSELSTSTDAQVKAFFK

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