GapMind for catabolism of small carbon sources

 

Protein WP_048081568.1 in Methanobacterium veterum MK4

Annotation: NCBI__GCF_000745485.1:WP_048081568.1

Length: 298 amino acids

Source: GCF_000745485.1 in NCBI

Candidate for 12 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 ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 90% 127.1 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 97% 116.3 GldA, component of The GldAFG putative ABC transporter required for ratchet-type gliding motility; may function in secretion of a macromolecule such as an exopolysaccharide. (Agarwal et al., 1997; Hunnicutt et al., 2002; McBride and Zhu 2013). Soluble GldG homologues (no TMSs) are found in eukaryotes (e.g. intraflagellar protein transporter, IPT52 of Chlamydomonas reinhardtii; XP_001692161) 36% 198.4

Sequence Analysis Tools

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Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIKIDSLTKYFGEIQALDNLSLNIKKGELLGIIGPNGAGKTTTIRIICGILKPDMGTVFV
GGHDVLEDPITTKSMIGYLPEEPNLYERFKARDLLRYFGELYGVPKEKLNDRVYELLELV
GMENRAEHKINTFSKGLRQRIGIARALIHDPEIIIFDEPTMGLDPATALSIRSFIEGLKG
EKTIILCTHYMEEADALCDRVAILSGGKIRDMGTPDYLKAKIHGQTILQIKMNHADIDTD
KVLNFNSVENVNLKGKNLEVSLNSKEDISDIVSLIGHNVVSVNTKEPSLEDVFIHAVK

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