Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate WP_011385236.1 AMB_RS14390 TIGR00730 family Rossman fold protein
Query= BRENDA::A0A2Z4EVE5 (218 letters) >NCBI__GCF_000009985.1:WP_011385236.1 Length = 193 Score = 171 bits (433), Expect = 9e-48 Identities = 85/180 (47%), Positives = 118/180 (65%) Query: 13 RRICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRHVI 72 +R+CVFCGS+ G +Y +AA +LG+ L R LVYGGG++GLMG+V+ A G VI Sbjct: 2 KRVCVFCGSNSGANPAYAKAAAQLGRLLAERGQVLVYGGGNVGLMGVVADAALAAGGQVI 61 Query: 73 GVIPKTLMPRELTGETVGEVKAVADMHQRKAEMARHSDAFIALPGGYGTLEELLEVITWA 132 GVIP++++ E+ + E++ VA MH+RKA MA +DAFIALPGG GTLEEL E+ TW Sbjct: 62 GVIPESMLKWEVGHPDLTELRVVASMHERKAAMADLADAFIALPGGIGTLEELFEIWTWG 121 Query: 133 QLGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPSARHIIVSAPTAKELVKKLEEYVP 192 QLG+H KP+G L+V GY+ L +F+D EGF+ R ++ L+ L+ Y P Sbjct: 122 QLGLHAKPLGFLDVAGYFERLHAFLDHMAAEGFVKARHREMVAVHNDPAILLALLDSYRP 181 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: 142 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: 193 Length adjustment: 21 Effective length of query: 197 Effective length of database: 172 Effective search space: 33884 Effective search space used: 33884 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