Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate GFF1879 PGA1_c19080 TIGR00730 family protein
Query= BRENDA::A0A2Z4EVE5 (218 letters) >FitnessBrowser__Phaeo:GFF1879 Length = 180 Score = 134 bits (337), Expect = 1e-36 Identities = 64/155 (41%), Positives = 94/155 (60%) Query: 11 RFRRICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRH 70 R +CV+CGS G + +Y +AA LG L ++ LVYG G +GLMG V++A G Sbjct: 2 RIHSVCVYCGSRDGVRPAYADAAEALGTGLATQGQRLVYGAGDVGLMGRVARAAQAAGGR 61 Query: 71 VIGVIPKTLMPRELTGETVGEVKAVADMHQRKAEMARHSDAFIALPGGYGTLEELLEVIT 130 GVIP+ L+ RE+ + MH+RK M ++DA + LPGG G+L+EL E +T Sbjct: 62 TFGVIPEHLVRREVAKTDLNTYVVTETMHERKKVMLYNADAVVVLPGGAGSLDELFEALT 121 Query: 131 WAQLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGF 165 W QL +H KP+ +LN+ GY++ L + ++ V EGF Sbjct: 122 WRQLELHGKPILILNIYGYWDPLKALVEHVVAEGF 156 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: 110 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: 218 Length of database: 180 Length adjustment: 20 Effective length of query: 198 Effective length of database: 160 Effective search space: 31680 Effective search space used: 31680 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 Apr 09 2024. 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