GapMind for catabolism of small carbon sources

 

Protein WP_012034880.1 in Methanocella arvoryzae MRE50

Annotation: NCBI__GCF_000063445.1:WP_012034880.1

Length: 256 amino acids

Source: GCF_000063445.1 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
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 38% 98% 177.2 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 34% 95% 148.7 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 94% 144.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 87% 142.1 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 87% 142.1 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 36% 93% 132.1 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-lysine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 36% 93% 132.1 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 33% 90% 130.2 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 96% 122.1 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 94% 119.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 94% 119.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 94% 119.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 94% 119.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 94% 119.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
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) 33% 76% 116.7 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 89% 114.8 Cobalamin import ATP-binding protein BtuD; Vitamin B12-transporting ATPase; EC 7.6.2.8 40% 187.2

Sequence Analysis Tools

View WP_012034880.1 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

MELKIDGLEVKYGSHKALDGVSFTVGEGEVVGVVGPNGSGKSTLIRCIAQIHKPSHGTVL
LNGRDALKMEPGEIARVIGYVPQNFHYLFFSTVMETVMLGRKPHIKWRVTPHDLAIVQQS
LEAMNIRHLADKFMDQLSGGEKQKVYIARALAQEPELFLFDEPTSNLDLKHQIDVLEITR
SLTRTGKKSMIVALHDLNLAVTYCDKILVLTRGKIYAAGKPEEILTPQTIKDVYGVDVFI
VESAYGRHILPIKAKA

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