GapMind for catabolism of small carbon sources

 

Protein WP_011384270.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS09430 ABC transporter ATP-binding protein

Length: 262 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 44% 89% 185.3 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 40% 58% 147.1 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 78% 146.7 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 54% 141 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 54% 141 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 54% 141 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 54% 141 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 38% 53% 140.6 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 66% 137.5 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 56% 130.6 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 34% 68% 129.4 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 66% 124.8 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 32% 76% 109 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 201.4

Sequence Analysis Tools

View WP_011384270.1 at NCBI

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MDALAPVSPPVIRLEGLAFGYPGDRSHAIVLQDLDLEVRHGDFIALVGQSGAGKSTLLRV
IAGLVPAVLGQVYVEPPKEPDSRQIGMVFQDARLLPWRRVLANVEYGLEGLVKSRHERRR
RALAALDLVGLTEFADRWPHHLSGGQRQRVGLARALAVRPALLLMDEPFGALDPATRHGL
QDQLLSIWQATGTSIIFVTHDIDEATYLADRVIVLGGSPARILRQLDVEAPRPRCRNDLA
DDPTATALRSQLYETFFYKDGI

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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