GapMind for catabolism of small carbon sources

 

Protein WP_043531485.1 in Halomonas xinjiangensis TRM 0175

Annotation: NCBI__GCF_000759345.1:WP_043531485.1

Length: 334 amino acids

Source: GCF_000759345.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 137.9
L-histidine catabolism natD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 31% 149.8
L-leucine catabolism natD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 31% 149.8
L-proline catabolism natD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 31% 149.8
L-serine catabolism braD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 137.9
L-threonine catabolism braD med NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 99% 180.6 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 137.9
L-isoleucine catabolism natD med NatD, 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% 98% 171.8 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 31% 149.8
L-valine catabolism natD med NatD, 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% 98% 171.8 High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine 31% 149.8
L-proline catabolism HSERO_RS00885 lo ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 31% 96% 168.3 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-isoleucine 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) 35% 88% 157.1 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
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) 35% 88% 157.1 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-leucine catabolism livH lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 88% 149.8 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-valine catabolism livH lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 88% 149.8 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 142.5 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 142.5 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 97% 142.5 NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE 34% 179.9

Sequence Analysis Tools

View WP_043531485.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNELVFFLNNVVVSGAVAGSIYAMGAIGVTLVFSIMRFAHFAHADMMTLGALLVLALTTL
FPEAGLAIGLPTAIVMLPVAMVITAIAAVGIDRVFYRPLRAHKVKPIVIVIGSLGVTLML
QGLIRLFAGTSAQSLYIAERKAIFRLEMPFELASRPVIITEPQVILFVLTLVAVVGLHLF
LSRSRLGKAMRAMSDNPDLARASGINTDTIVAVTWIIAGGLAAVAGTLLSLDVAFKPDLS
FFLLLPIFAAAIVGGVGHPYGAIAGGFVIGFAETLAVFNWSVLLRPLRDSFPTWLELPNN
LALVGTEYKIVVPFFILVAILVWRPTGIFKGKVI

This GapMind analysis is from Sep 24 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