GapMind for catabolism of small carbon sources

 

Protein CA265_RS01140 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS01140 ABC transporter

Length: 229 amino acids

Source: Pedo557 in FitnessBrowser

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-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 37% 67% 152.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 90% 148.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 90% 148.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 90% 148.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 84% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 90% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 36% 90% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 80% 132.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
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% 73% 118.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 51% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 82% 101.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 197.6

Sequence Analysis Tools

View CA265_RS01140 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MESILNIRNVSKIYQSAGRELTVLDNINFSITAGSTVAITGPSGSGKTTLLGLCAGLDRA
SSGTVELNGIALEKLNEDERAAVRNQYVGFIFQNFQLLPTLTALENVMVPLELRGAKNIR
AHALELLDKVGLADRSHHYPVQLSGGEQQRVSLARAFSNQPAILFADEPTGNLDAETSEK
VIKLLFDLNKDAGTTLIIVTHDLELAARTARSIKIKGGVIISDENSTYA

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 preprint 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