GapMind for catabolism of small carbon sources

 

Protein WP_061533926.1 in Collimonas arenae Ter10

Annotation: NCBI__GCF_001584165.1:WP_061533926.1

Length: 242 amino acids

Source: GCF_001584165.1 in NCBI

Candidate for 16 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 BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 96% 254.2 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 96% 254.2 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 56% 96% 254.2 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 51% 94% 248.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 53% 95% 247.3 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
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) 51% 98% 244.6 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 53% 91% 237.7 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 53% 91% 237.7 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 48% 99% 232.3 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
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) 50% 89% 223.8 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 47% 98% 211.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 47% 98% 211.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-glutamate catabolism gltL med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 47% 98% 211.1 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 72% 174.9 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 89% 144.4 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 39% 82% 142.5 Amino acid ABC transporter ATP binding protein, component of Hydroxy L-proline uptake porter, HprABC 56% 257.7

Sequence Analysis Tools

View WP_061533926.1 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

MPLIAIDNVKKSFGDNQVLKGIRLDVEPGEVIAIIGKSGSGKSTLLRCINGLESIDEGNI
SVAGSHLGKTELELRALRLKVGMIFQQFNLFPHLTVGRNVMLSPMIVKGTSESEARKSAQ
ENLARVGLAEKFDAYPDQLSGGQQQRVAIARALTMQPQALLCDEITSALDPELVNEVLTV
VRGLAEEGMTLLMVTHEMRFAREVCDRVVFMHQGKVHEIGPPEDIFANPKTLELQQFLGA
SH

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