Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate CA265_RS10665 CA265_RS10665 Rossman fold protein, TIGR00730 family
Query= BRENDA::A0A2Z4EVE5 (218 letters) >FitnessBrowser__Pedo557:CA265_RS10665 Length = 197 Score = 161 bits (408), Expect = 7e-45 Identities = 76/188 (40%), Positives = 125/188 (66%) Query: 10 SRFRRICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDGGR 69 ++ +CV+CGS+ + ++A +L + LV + I L+YGGGS+G+MG+++ V + G Sbjct: 2 NKLNSVCVYCGSNFNGDITLRKAIKQLAETLVKQQIRLIYGGGSVGVMGVLANDVLELGG 61 Query: 70 HVIGVIPKTLMPRELTGETVGEVKAVADMHQRKAEMARHSDAFIALPGGYGTLEELLEVI 129 V GVIP+ LM +E+ + + E+ +MHQRK +MA SD F+ LPGG+GTLEE EV+ Sbjct: 62 LVTGVIPQFLMDKEVGHQGLTEMVVTENMHQRKQKMADLSDGFVILPGGFGTLEEFFEVL 121 Query: 130 TWAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPSARHIIVSAPTAKELVKKLEE 189 TW QLG+H+KP+G+LNV G+Y+ L + +D V+ F+ P+ R ++ + A+ L+ K++ Sbjct: 122 TWLQLGLHNKPIGVLNVSGFYDPLFAQMDMMVQSKFLKPANRDLVFNEADAEILIHKMDG 181 Query: 190 YVPSHESV 197 + S + V Sbjct: 182 FSASPDEV 189 Lambda K H 0.316 0.134 0.383 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: 146 Number of extensions: 7 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: 218 Length of database: 197 Length adjustment: 21 Effective length of query: 197 Effective length of database: 176 Effective search space: 34672 Effective search space used: 34672 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: 45 (21.9 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