GapMind for catabolism of small carbon sources

 

Protein BWI76_RS26345 in Klebsiella michiganensis M5al

Annotation: BWI76_RS26345 branched-chain amino acid ABC transporter permease LivH

Length: 308 amino acids

Source: Koxy in FitnessBrowser

Candidate for 20 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 hi branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized) 97% 100% 577.8 L-proline and D-alanine ABC transporter, permease component 1 55% 335.5
L-leucine catabolism livH hi branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized) 97% 100% 577.8 L-proline and D-alanine ABC transporter, permease component 1 55% 335.5
L-phenylalanine catabolism livH hi branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized) 97% 100% 577.8 L-proline and D-alanine ABC transporter, permease component 1 55% 335.5
L-valine catabolism livH hi branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized) 97% 100% 577.8 L-proline and D-alanine ABC transporter, permease component 1 55% 335.5
L-alanine catabolism braD med High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 67% 99% 404.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-serine catabolism braD med High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 67% 99% 404.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-threonine catabolism braD med High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 67% 99% 404.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
D-alanine catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 55% 99% 335.5 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-proline catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 55% 99% 335.5 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-arginine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 99% 300.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-glutamate catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 99% 300.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-histidine catabolism braD med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 99% 300.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-proline catabolism HSERO_RS00885 med ABC transporter permease (characterized, see rationale) 43% 99% 250.4 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-serine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 43% 99% 250.4 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-tyrosine catabolism Ac3H11_1695 med ABC transporter permease (characterized, see rationale) 43% 99% 250.4 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
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) 30% 97% 157.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
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) 30% 97% 157.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
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) 30% 97% 157.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
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) 30% 97% 157.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8
L-histidine catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 154.1 branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) 97% 577.8

Sequence Analysis Tools

View BWI76_RS26345 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSEQFLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAA
LMMMGIDTSWLLVAAGFVGAIVIASAYGWSIERVAYRPVRSSKRLIALISAIGMSIFLQN
YVSLTEGSRDVALPSLFNGQWTVGSSDNFSATITTMQLVIWVVTFIAMLALTLFIRYSRM
GRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGM
KAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGIL
GRPEVEKV

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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