GapMind for catabolism of small carbon sources

 

Protein CA265_RS04345 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD

Length: 216 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 61 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 Arginine transport ATP-binding protein ArtM (characterized) 43% 90% 163.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 89% 153.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 39% 58% 147.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 89% 143.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 89% 143.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 83% 141.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 83% 141.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 35% 55% 137.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 37% 89% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 34% 60% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 85% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 83% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 85% 134.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 60% 132.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 57% 131.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 84% 131 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 33% 63% 127.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 33% 63% 127.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 30% 62% 122.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 73% 115.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 87% 109.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 91% 109.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 91% 105.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 90% 103.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 90% 103.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 102.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 102.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 102.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 31% 86% 100.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 86% 99 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 86% 99 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 86% 99 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 85% 98.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 85% 98.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 85% 98.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 85% 98.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 33% 64% 89.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 50% 88.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2

Sequence Analysis Tools

View CA265_RS04345 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

MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL
KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE
LLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQLF
VSLRDNFHQTFVIVTHNEHLAKTSDRVVSMKDGLIV

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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