GapMind for catabolism of small carbon sources

 

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

Annotation: FitnessBrowser__Pedo557:CA265_RS04345

Length: 216 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 63 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
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 61% 139 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 61% 139 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 47% 207.2
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 61% 139 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
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 37% 81% 131.7 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
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

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL
KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAKTNKKQAETRAFE
LLDLFGLKDRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGLHQLF
VSLRDNFHQTFVIVTHNEHLAKTSDRVVSMKDGLIV

This GapMind analysis is from Apr 09 2024. 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