GapMind for catabolism of small carbon sources

 

Protein WP_013835621.1 in Thiomicrospira cyclica ALM1

Annotation: NCBI__GCF_000214825.1:WP_013835621.1

Length: 234 amino acids

Source: GCF_000214825.1 in NCBI

Candidate for 38 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 84% 141.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 84% 141.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 84% 141.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 90% 139 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
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) 37% 85% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-asparagine catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-aspartate catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-glutamate catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-histidine catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-leucine catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-proline catabolism aapP lo 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) 38% 81% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 36% 86% 136.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 36% 86% 136.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 34% 59% 136.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 35% 91% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 87% 130.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 87% 130.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 86% 129 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 56% 128.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 56% 128.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 60% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 86% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 86% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 60% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 52% 124 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 56% 121.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 34% 53% 119 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 77% 118.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 34% 87% 118.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 93% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7
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) 31% 69% 99.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 54% 245.7

Sequence Analysis Tools

View WP_013835621.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSKSDSVILQAQGLSQVFQEGLLATPVLHDINFSLHAGERLAIVGASGSGKSTLLHLLAG
LAQPSEGEVFLQGQAFASLSEAQRSQLRNQHLGFVYQFHYLLAELTALENVMLPLRIARV
PAKQAQHKAQELLAAVGLAARADHKPSELSGGERQRVAIARALITEPACILADEPTGNLD
SKSAEQVLALMLNLNEQFNTALLVVTHDLQLAKQLGNKIELVDGQIQRDNDANA

This GapMind analysis is from Apr 09 2024. 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