GapMind for catabolism of small carbon sources

 

Protein WP_012466358.1 in Chlorobium limicola DSM 245

Annotation: NCBI__GCF_000020465.1:WP_012466358.1

Length: 244 amino acids

Source: GCF_000020465.1 in NCBI

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 40% 89% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 90% 136.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 90% 136.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-glutamate catabolism gltL med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 90% 136.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-lysine catabolism hisP med ABC transporter for L-Lysine, ATPase component (characterized) 40% 91% 133.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 67% 158.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 67% 139.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 38% 92% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 63% 135.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 32% 71% 128.6 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 55% 112.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 62% 109.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 31% 62% 109.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 36% 91% 107.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 36% 91% 107.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 105.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 105.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 97% 105.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 94% 97.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 94% 97.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 94% 97.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 31% 55% 94.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 91% 91.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 46% 189.5

Sequence Analysis Tools

View WP_012466358.1 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

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Sequence

MQDNSSGSVSHQAVLSIQDLSKTYIMGEVKVEALKHLSIEFFAGELVVLLGASGSGKSTL
LNIIGGLDLPSEGKLFFQGREITAATEAELTAYRRRSIGFVFQFYNLISSLSALENVQLV
TEIADNPMPADEALRLVGLSNRLNHFPAQLSGGEQQRVAIARAVAKKPELLLCDEPTGAL
DYQTGKLVLEVIEKVNRELGTTTIVITHNASIAGMADRVVRLGSGEVTEDRRNPERLTPA
ELVW

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