Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate Ga0059261_2416 Ga0059261_2416 TIGR00730 family protein
Query= BRENDA::A0A2Z4EVE5 (218 letters) >FitnessBrowser__Korea:Ga0059261_2416 Length = 196 Score = 147 bits (370), Expect = 2e-40 Identities = 72/180 (40%), Positives = 108/180 (60%) Query: 14 RICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRHVIG 73 R+ ++CGS+ Y E A +G+ L R I +VYGGG +GLMG V+ A + G VIG Sbjct: 6 RLAIYCGSATPSDPVYVENARFVGRTLAERGIGVVYGGGRLGLMGAVADAALEAGGEVIG 65 Query: 74 VIPKTLMPRELTGETVGEVKAVADMHQRKAEMARHSDAFIALPGGYGTLEELLEVITWAQ 133 VIP+ L+ E+ E+ V MH+RK SD F+ LPGG GT++EL E ++WAQ Sbjct: 66 VIPQALVDAEVAHRGCTELHIVRTMHERKQAFTDISDGFVTLPGGTGTMDELWEAMSWAQ 125 Query: 134 LGIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPSARHIIVSAPTAKELVKKLEEYVPS 193 +G H KPVGLLN +Y+ L++F+ E GF+ P + +++ L++K+ +VP+ Sbjct: 126 IGYHAKPVGLLNTANFYDGLIAFVKTMGEVGFLRPQHQGLLIIDDQLDGLLEKMAAHVPA 185 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: 162 Number of extensions: 5 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: 196 Length adjustment: 21 Effective length of query: 197 Effective length of database: 175 Effective search space: 34475 Effective search space used: 34475 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