Align Arginine decarboxylase proenzyme; ADC; ArgDC; EC 4.1.1.19; Pyruvoyl-dependent arginine decarboxylase (uncharacterized)
to candidate WP_008496469.1 B481_RS02560 S-adenosylmethionine decarboxylase proenzyme
Query= curated2:C3N6F7 (134 letters) >NCBI__GCF_000342445.1:WP_008496469.1 Length = 127 Score = 73.2 bits (178), Expect = 1e-18 Identities = 36/99 (36%), Positives = 62/99 (62%), Gaps = 3/99 (3%) Query: 21 IGKHVFGNLYDIDAERLNDKEFLEKLVLEAVNIAHMKLVEIKAWSFGGKKGGVSVIALVE 80 +G+HV L+ D ++LND +F+E+ ++A + ++ E+ F + GVS + ++ Sbjct: 4 MGRHVIAELWQCDFDKLNDMDFIEQTFVDAALKSGAEVREVAFHKFAPQ--GVSGVVIIS 61 Query: 81 ESHIALHTWNEYNYATLDVYTCGEDSDPQSAFAHIVNAL 119 ESH+ +H++ E+ YA++DVYTCG D DP A +I AL Sbjct: 62 ESHLTIHSFPEHGYASVDVYTCG-DLDPTIAAEYIAEAL 99 Lambda K H 0.315 0.132 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 49 Number of extensions: 2 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 134 Length of database: 127 Length adjustment: 14 Effective length of query: 120 Effective length of database: 113 Effective search space: 13560 Effective search space used: 13560 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 41 (20.4 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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