GapMind for catabolism of small carbon sources

 

Protein WP_011385250.1 in Magnetospirillum magneticum AMB-1

Annotation: NCBI__GCF_000009985.1:WP_011385250.1

Length: 286 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-lactate catabolism PGA1_c12660 lo D-lactate transporter, permease component 2 (characterized) 36% 74% 162.5 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-phenylalanine catabolism livH lo Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) 30% 97% 145.6 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-alanine catabolism braD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
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% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-leucine catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-proline catabolism natD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-serine catabolism braD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1
L-threonine catabolism braD lo NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 97% 127.9 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 36% 174.1

Sequence Analysis Tools

View WP_011385250.1 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

MDFWFFLIQVLNGVQYGLLLFLVASGLTLIFGIMGIINLAHGAFYMLGAYLAYWLARTTG
SLGAAVLLSLPIAAAIGYGIEALLVRTLYRRDHLDQVLLTYGLILIFNEATRMIWGADVH
GVAVPAALNWSIRLTDTLSYPVYRLMLSGVCAVLAVGMYLVITRTRFGMWVRAGASNRDM
VAALGINVKLLFGVVFALGAALAGLAGAISTPITSVAPGMGDSVLILCFVVVVIGGVGSI
KGAFLGAMLIGLADTFGKVFAPDFASFTVYGVMAAVLLWKPRGLFS

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 (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