GapMind for catabolism of small carbon sources

 

Protein WP_041415807.1 in Shewanella halifaxensis HAW-EB4

Annotation: NCBI__GCF_000019185.1:WP_041415807.1

Length: 302 amino acids

Source: GCF_000019185.1 in NCBI

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 livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 118.6 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 118.6 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 118.6 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-alanine catabolism braG lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-isoleucine catabolism natE lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-leucine catabolism natE lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-proline catabolism natE lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-serine catabolism braG lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-threonine catabolism braG lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-valine catabolism natE lo NatE, 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% 89% 105.9 Probable ABC transporter ATP-binding protein NosF 41% 225.7
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 94% 102.1 Probable ABC transporter ATP-binding protein NosF 41% 225.7

Sequence Analysis Tools

View WP_041415807.1 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

MSELAIQLTDVSLKYNDFTALDGVSFDVEAGQTMALLGHNGAGKSSLIKIILGLIMPTSG
TVNILGQNAQESQAHNSVRLGYLPEDANFYDKLTGCEVLSYFAALKGVNQPRVASLIEEF
GLEYAQHRQLKTYSKGMKQRLGVAQAILSEPKVLLLDEPTVGLDPQASQFLYGKINQLKL
AGCAVVISTHELSLAESHLDRALIMAKGKRLAIGSCAELRNASSIKTRIHFSELSERVKT
NAYLQQFYQDGLLQFDADKKVDIVKHLVSQCQIFDFEIKEPRLEDIYHDLMGQSLRSSVE
QS

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