GapMind for catabolism of small carbon sources

 

Protein WP_037155449.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_037155449.1

Length: 359 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 58% 98% 401.4 Maltose-transporting ATPase (EC 3.6.3.19) 56% 393.3
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 56% 96% 393.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 55% 98% 389.8 Maltose-transporting ATPase (EC 3.6.3.19) 56% 393.3
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 57% 99% 389 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 56% 93% 378.6 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 98% 370.5 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 98% 370.5 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 98% 370.5 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 55% 98% 370.5 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 52% 96% 335.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 51% 99% 334 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 97% 322.8 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 49% 94% 313.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 53% 76% 258.8 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 401.4

Sequence Analysis Tools

View WP_037155449.1 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

MATSVSLQKVIKRYGELQVVHGIDLEIEPGEFTVFVGPSGCGKSTLLRMIAGLEPISGGG
LYLDGSRMNDVPASKRGIAMVFQSYALYPHMTVYKNLAFGLETAGMKKHEIQPRVEKAAE
VLQITQLLQRKPKQLSGGQRQRVAIGRAIVREPNIFLFDEPLSNLDAELRVQMRVEIARL
HQRLGNTMIYVTHDQTEAMTMADKIVVLNGGKIEQVGAPLDLYNKPKNKFVAGFIGSPKM
NFLDAKIVGSDDGSAVIDLAGQTVRLPRRLGGLQPGQPVTLGARPEHLNVGDRGLSLGDA
RVDLVEHLGGQTILYVTLHGGQALTIALEDQQAIRAGETVSIHIDPERCHLFGPDGVTL

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