GapMind for catabolism of small carbon sources

 

Protein SM_b20785 in Sinorhizobium meliloti 1021

Annotation: SM_b20785 branched-chain amino acid ABC transporter ATP-binding protein

Length: 254 amino acids

Source: Smeli 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 livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 39% 98% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 39% 98% 173.7 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 38% 100% 169.5 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 38% 100% 169.5 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 164.1 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 164.1 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 38% 98% 164.1 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 161.4 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 161.4 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 38% 97% 161.4 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 37% 100% 159.8 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 100% 490.3

Sequence Analysis Tools

View SM_b20785 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

MSAIFEVRNLKRSFGGLAVTNDVSLSMAPGDRVALIGPNGAGKTTFVNLVTGNLKPDAGE
VRIGGETVTNVDAIGRVRRGLVRSFQVTRLFQDMTPAEHVALAVLQRDGRAGRMFGNFLA
MPGVMAEAGSLLGKLGLRDLAHRPVREIAYGQQRLLEIAVALALKPRVLLLDEPAAGVPQ
SDTGRIEQALADLPDDLAVLMIEHDMDLVFRFAKRVIVLAAGTVIFDGSPADVTKDPRVR
EAYLGSYADAGSAA

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