GapMind for catabolism of small carbon sources

 

Protein 8501892 in Desulfovibrio vulgaris Miyazaki F

Annotation: FitnessBrowser__Miya:8501892

Length: 372 amino acids

Source: Miya in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braC med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 34% 222.6
L-isoleucine catabolism livJ med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4
L-leucine catabolism livJ med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4
L-serine catabolism braC med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 34% 222.6
L-threonine catabolism braC med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 34% 222.6
L-valine catabolism livJ med Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 37% 100% 243.4 leucine-specific-binding protein LivK 33% 219.9
L-phenylalanine catabolism livJ med Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale) 36% 95% 239.2 BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 33% 190.7
D-alanine catabolism AZOBR_RS08260 lo Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 33% 99% 218 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 37% 243.4
L-proline catabolism AZOBR_RS08260 lo Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 33% 99% 218 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 37% 243.4
L-arginine catabolism braC lo BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 33% 94% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 37% 243.4
L-glutamate catabolism braC lo BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 33% 94% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 37% 243.4
L-histidine catabolism braC lo BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 33% 94% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 37% 243.4

Sequence Analysis Tools

View 8501892 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

MRKGWFKGLVAGLAVAVMACPAFAADTIKFGVAGAHSGDLASYGLPTVNAAKLVAKMINA
KGGVLGKQVEVIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEANIV
LMSPSATNPALTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGKGY
AEYAKQFVEQSGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQQL
RKKRMDLPFVSDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGAEP
GAFYKEAYAASLALLNAIEKAGSTDSAKIMNALRTEFVETSVGKIKFDKRGDAEGVGFSM
YQVKNGKYVELK

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