GapMind for catabolism of small carbon sources

 

Protein 353166 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Length: 218 amino acids

Source: Btheta in FitnessBrowser

Candidate for 40 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) 42% 90% 171.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 90% 153.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-asparagine catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 37% 89% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-aspartate catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 37% 89% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 56% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 36% 83% 147.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 61% 146 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 36% 87% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 63% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 59% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 58% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
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) 35% 82% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 87% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 58% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 33% 57% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 77% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 77% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 86% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 90% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 90% 107.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 31% 89% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 78% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 32% 89% 100.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 95.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 95.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 95.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 95.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 95.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 207.6

Sequence Analysis Tools

View 353166 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAI
DGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAME
ILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLF
FDLRDRLGQTFVIVTHDEGLAKITDRTVHMVDGTIKKD

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, 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