GapMind for catabolism of small carbon sources

 

Protein WP_034268201.1 in Amycolatopsis halophila YIM 93223

Annotation: NCBI__GCF_000504245.1:WP_034268201.1

Length: 291 amino acids

Source: GCF_000504245.1 in NCBI

Candidate for 18 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 med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 165.6 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 164.9
L-leucine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 165.6 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 164.9
L-valine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 98% 165.6 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 164.9
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 99% 149.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 99% 149.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 99% 149.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 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) 33% 96% 149.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 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) 33% 96% 149.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 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) 33% 96% 149.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-phenylalanine catabolism livH lo ABC transporter permease (characterized, see rationale) 31% 98% 146.7 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-proline catabolism HSERO_RS00885 lo ABC transporter permease (characterized, see rationale) 31% 98% 146.7 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-serine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 31% 98% 146.7 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-tyrosine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 31% 98% 146.7 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-isoleucine catabolism natD lo 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) 32% 97% 144.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-leucine catabolism natD lo 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) 32% 97% 144.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-proline catabolism natD lo 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) 32% 97% 144.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-valine catabolism natD lo 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) 32% 97% 144.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6
L-histidine catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 98% 133.3 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 32% 165.6

Sequence Analysis Tools

View WP_034268201.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSGLLQQLFNGLVSGSFYALLALGLSVIFGMLGVVNFAHGAFYMLGAFGAFVLLDSAGLS
WWLALLVVPILLGVIGMVLERLFVHRLMHLFPLYNFLLTFGIALILQDLIRMKYGVTSQP
YARPSILDGSVDLGLFTYPKYQVFVFVFSIALSGLVWLVLSRTRVGMIVRASTERAELTQ
SLGIDVRRWVTPVFGFGIALAGLAGVLAAPMRAVNSSMGADLIIVIFAVVVIGGLGSVLG
SVAAGYIVGMVTAIGNFYVPALSQSLVFVLMALVLLLRPAGLFGREEGVHA

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