GapMind for catabolism of small carbon sources

 

Protein WP_053544758.1 in Corynebacterium deserti GIMN1.010

Annotation: NCBI__GCF_001277995.1:WP_053544758.1

Length: 254 amino acids

Source: GCF_001277995.1 in NCBI

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 55% 95% 268.1 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 54% 99% 267.7 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-arginine catabolism artP med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 54% 98% 267.3 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 54% 98% 267.3 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
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) 52% 97% 261.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 53% 92% 259.6 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 53% 92% 259.6 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 53% 100% 256.5 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 53% 100% 256.5 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 52% 93% 255.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 52% 93% 255.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 53% 96% 253.8 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 54% 94% 248.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 51% 100% 248.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 51% 100% 248.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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) 51% 95% 246.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 51% 96% 246.5 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 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% 92% 235.3 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 47% 99% 226.5 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 47% 99% 226.5 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 72% 162.9 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 129.4 NocP aka ATU6028 aka AGR_PTI_69, component of Nopaline porter 54% 274.2

Sequence Analysis Tools

View WP_053544758.1 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

MSQLMIDAQQVCKNYGRLEVLKGIDLQVPKGTVTCLIGPSGSGKSTMLRCVNHLEKVNAG
RLYVDGDLIGYRERDGVLYEISEKDAAKQRSDIGMVFQNFNLFPHRTVIENIIEAPIHVK
KQPESKARARAMELLEQVGLAHKADAYPVQLSGGQQQRVAIARAVAMEPKLMLFDEPTSA
LDPELVGEVLRVMKQLADDGMTMLVVTHEMGFAHEVADQVVFMADGVVVEAGTPEQVLDN
PREQRTKDFLSSLL

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