GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02378 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_02378 amino acid/amide ABC transporter membrane protein 1, HAAT family

Length: 294 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 157.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-leucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 157.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-valine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 33% 97% 157.1 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-proline catabolism HSERO_RS00885 lo ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 30% 98% 146.4 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 98% 146 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 98% 146 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 98% 146 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-alanine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 140.6 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-serine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 140.6 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-threonine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 140.6 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6
L-phenylalanine catabolism livH lo Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) 31% 97% 140.2 ABC transporter, permease, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 32% 165.6

Sequence Analysis Tools

View H281DRAFT_02378 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MDIFGIPLPAMLSQLLLGLVNGSFYAILSLGLAVIFGLLNVINFAHGALFMLGAMLAWMG
FSYFGVPYWAMLVLAPLIVGLFGVAIERSMLRWLYKLDHLYGLLLTFGLTLVVEGVFRSI
YGSSGQPYDVPSALSGATNLGFMFLPNYRAWVVVASLIVCFATWFVIEKTRLGAYLRAGT
ENPKLVEAFGINVPLMITLTYGFGVALAAFAGVLAAPVIQVSPLMGQPMIITVFAVVVIG
GMGSIMGSILTGLMLGVIEGLTRVFYPEASATVVFVIMALVLLVRPAGLFGKEK

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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