Align Arginine decarboxylase proenzyme; ADC; ArgDC; EC 4.1.1.19; Pyruvoyl-dependent arginine decarboxylase (uncharacterized)
to candidate Synpcc7942_2249 Synpcc7942_2249 S-adenosylmethionine decarboxylase proenzyme
Query= curated2:Q9YG22 (132 letters) >FitnessBrowser__SynE:Synpcc7942_2249 Length = 141 Score = 87.4 bits (215), Expect = 7e-23 Identities = 44/119 (36%), Positives = 64/119 (53%), Gaps = 2/119 (1%) Query: 9 VGKHVYGSLYGVPREKATDEEYLRGVVVRAAESAGATVHAVNSWTIPGEKGGVSVIVLVL 68 VG H LYG P E D + ++ + AA AGAT+ E GV+ + L+ Sbjct: 17 VGTHCILELYGCPAELLNDADQIQANLRAAATEAGATLLQETCHRF--EPQGVTALALLA 74 Query: 69 ESHLALHTWPEYDYATFDIYTCGEHTDPWKAFELLLSELKPRKYTVHYVDRSQEKTVLE 127 ESH+++HTWPE YA D++TCG HT P A L+ + R+YT+H + R ++ E Sbjct: 75 ESHISIHTWPESGYAAVDVFTCGSHTQPETACHFLIEAFRSRQYTLHTLRRQPPASIRE 133 Lambda K H 0.317 0.134 0.407 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: 82 Number of extensions: 3 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: 132 Length of database: 141 Length adjustment: 15 Effective length of query: 117 Effective length of database: 126 Effective search space: 14742 Effective search space used: 14742 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: 42 (20.8 bits)
This GapMind analysis is from Sep 17 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