Align Arginine decarboxylase proenzyme; ADC; ArgDC; EC 4.1.1.19; Pyruvoyl-dependent arginine decarboxylase (uncharacterized)
to candidate AZOBR_RS02015 AZOBR_RS02015 S-adenosylmethionine decarboxylase
Query= curated2:A2BM05 (142 letters) >FitnessBrowser__azobra:AZOBR_RS02015 Length = 169 Score = 73.6 bits (179), Expect = 1e-18 Identities = 39/105 (37%), Positives = 64/105 (60%), Gaps = 4/105 (3%) Query: 16 GDLIVGKHVYGNLYGVDEEKLWDEELLKDIVVEAARVANMNLVDIKTWKFTGFHGGVSVI 75 G + G H+ +L+G E+L + + ++ ++E+ VA L+ I FT +GG+S + Sbjct: 54 GKVCAGTHLIVDLWGA--ERLDELDHVRSTLIESVEVAGATLLHIHLHHFTP-NGGISGV 110 Query: 76 ALVLESHISIHTWPDYGYATVDVYTCGANSDPWKAFNYIVLKLKP 120 A++ ESHISIHTWP+ GYA +D++ CG ++ P KA + KP Sbjct: 111 AVLAESHISIHTWPERGYAALDIFMCG-DAQPMKAIPVLERAFKP 154 Lambda K H 0.318 0.137 0.426 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: 71 Number of extensions: 3 Number of successful extensions: 1 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: 142 Length of database: 169 Length adjustment: 17 Effective length of query: 125 Effective length of database: 152 Effective search space: 19000 Effective search space used: 19000 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 (21.7 bits) S2: 43 (21.2 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