GapMind for catabolism of small carbon sources

 

Protein 207079 in Desulfovibrio vulgaris Hildenborough

Annotation: MicrobesOnline__882:207079

Length: 241 amino acids

Source: 882 in MicrobesOnline

Candidate for 38 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 169.9 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 38% 98% 164.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
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) 36% 100% 154.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
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) 36% 100% 154.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
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) 36% 100% 154.5 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 93% 151 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 93% 151 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 36% 93% 151 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 98% 148.3 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-isoleucine catabolism natA lo NatA, 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) 36% 97% 146.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-valine catabolism natA lo NatA, 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) 36% 97% 146.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 143.3 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 96% 143.3 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 34% 99% 140.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 91% 135.2 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 89% 134.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 89% 134.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 89% 134.4 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 94% 132.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 94% 132.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 35% 94% 132.1 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 131.7 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 131.7 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 97% 131.7 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 34% 88% 131 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 94% 131 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 34% 88% 131 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 94% 131 lipopolysaccharide ABC transporter, ATP-binding protein LptB; EC 3.6.3.- 56% 266.9

Sequence Analysis Tools

View 207079 at MicrobesOnline

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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

MMAVLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGI
VRLDGQDIADWPLHERARVGLSYLPQESSVFKRLTVRENLEIILEHTGLPAARQKERAEA
LMADFGIAHLASSRAMHLSGGERRRLEIARCMIREPKFVLLDEPFAGIDPLAVGDIQGLI
RKLRDRGIGVLISDHNVRETLTICDRAYLVHQGQVILDGTPEHIVGDEQARLVYLGADFC
L

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:

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