GapMind for catabolism of small carbon sources

 

Protein WP_011385204.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS14215 FAA hydrolase family protein

Length: 340 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 5 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism KDF-hydrolase med L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized) 38% 88% 174.5 2,4-dihydroxy-5-methyl-6-oxohexa-2,4-dienoate isomerase 35% 153.3
L-rhamnose catabolism LRA6 med L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized) 38% 88% 174.5 2,4-dihydroxy-5-methyl-6-oxohexa-2,4-dienoate isomerase 35% 153.3
D-xylose catabolism HDOP-hydrol lo FAA hydrolase family protein (characterized, see rationale) 36% 97% 165.2 Ureidoglycolate lyase; UGL; Ureidoglycolase; Ureidoglycolatase; Ureidoglycolate hydrolase; EC 4.3.2.3 37% 169.9
L-phenylalanine catabolism fahA lo fumarylacetoacetase (EC 3.7.1.2) (characterized) 35% 76% 119.4 L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase 38% 174.5
L-tyrosine catabolism fahA lo fumarylacetoacetase (EC 3.7.1.2) (characterized) 35% 76% 119.4 L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase 38% 174.5

Sequence Analysis Tools

View WP_011385204.1 at NCBI

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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MDEKRRQFLTLGAGVAAGALLTRAAGAAGPIPNSAAGALRLVTYSAGGVAPRVGVVKASG
RVVDLGAAAKARGMALAFDPASMVSLIRAGDFALAQARQLMQEGPETGPLVSEVRLLAPI
PEPSRNVYAVGWNYLEHFKEGEAMRLKSADLPEHPVFFTKAVGTVNGPYDPIPYDAAVST
SIDWECELAVIIGKGGKNIAEADAMKHVFGFCVINDTTARDVQQKKHGGQWFKGKSLDGH
GPLGPWIVPASDIDHTRVHLITRVNGVVKQDASTEQMYFKVPRIIAELSAGLTLEPGDII
ATGTPPGVGGARKPPEFLKPGDVMETEIVEIGLLRNVIGG

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, the preprint on GapMind for carbon sources, 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