Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate 3608365 Dshi_1767 hypothetical protein (RefSeq)
Query= BRENDA::A0A2Z4EVE5 (218 letters) >FitnessBrowser__Dino:3608365 Length = 179 Score = 140 bits (352), Expect = 2e-38 Identities = 71/160 (44%), Positives = 94/160 (58%) Query: 15 ICVFCGSSQGKKTSYQEAAIELGKELVSRNIDLVYGGGSIGLMGLVSQAVHDGGRHVIGV 74 ICVFCG+ G S+ + A LG+ L LVYG G +GLMG V++A G GV Sbjct: 4 ICVFCGARAGLTPSHTDTAEALGRWLAEAGHRLVYGAGDVGLMGSVARAAQQAGGDTFGV 63 Query: 75 IPKTLMPRELTGETVGEVKAVADMHQRKAEMARHSDAFIALPGGYGTLEELLEVITWAQL 134 IP L+ E+ + MH+RK M +SDA + LPGG G+L+E EV+TW QL Sbjct: 64 IPAHLLDLEVGKTDLTRFVVTETMHERKKVMFANSDAIVVLPGGAGSLDEFFEVLTWRQL 123 Query: 135 GIHDKPVGLLNVDGYYNSLLSFIDKAVEEGFISPSARHII 174 G+H KP+ LLNVDGY+ LL+ ID + +GF + S R I Sbjct: 124 GLHAKPILLLNVDGYWTPLLALIDHVIAQGFAAESLRGFI 163 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: 119 Number of extensions: 4 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: 179 Length adjustment: 20 Effective length of query: 198 Effective length of database: 159 Effective search space: 31482 Effective search space used: 31482 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