Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate WP_086509880.1 BZY95_RS10510 FAD-binding oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >NCBI__GCF_002151265.1:WP_086509880.1 Length = 431 Score = 148 bits (374), Expect = 3e-40 Identities = 113/359 (31%), Positives = 159/359 (44%), Gaps = 4/359 (1%) Query: 29 GEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRPDD 88 G + DVCV+GGGITG SAA+HL E+G SV +LEA +IG G SGR+ G + G Sbjct: 31 GHQRVDVCVVGGGITGCSAALHLAERGYSVALLEAHEIGFGASGRSGGQILPGLGTDIAT 90 Query: 89 VEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHE 148 VE LG+++ ++ ++ EA +IER I C G LH A + +L E Sbjct: 91 VEQALGRERARQVWEMSREAVRLTAELIERHAIPCDLAW-GYLHAAVKPRHVRELRQFQE 149 Query: 149 QWRRRGADVEL--LTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKI 206 + R L L G +E TD AL D G ++P+ YT GLA A + G I Sbjct: 150 RMARDYGYEALAWLEGEALRERVVTDAYPGALFDSEGGHLHPLNYTLGLARAAQQAGVAI 209 Query: 207 FQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVASK 266 + S + R G V T RG + A+ VV+ AY L R Y VA++ Sbjct: 210 HEHSPALDV-RRGQPATVVTERGEITADFVVVGANAYLGRLLPELDGHIMRAANYIVATE 268 Query: 267 PLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQS 326 PL A +VLP+ D VL R RL+ G D + ++ D + Sbjct: 269 PLGEARASQVLPYNDAISDANFVLDYYRLSADKRLIYGGEVSYDGREPRGLQRRMDAKIA 328 Query: 327 HYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAE 385 +P L V + W G + T + + GY+G G + G+ AE Sbjct: 329 RLFPLLEGVRIDYRWGGDVAITLNRAPDFGRLGANVYYAQGYSGHGMALAGLAGKLLAE 387 Lambda K H 0.319 0.135 0.419 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: 449 Number of extensions: 25 Number of successful extensions: 3 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: 432 Length of database: 431 Length adjustment: 32 Effective length of query: 400 Effective length of database: 399 Effective search space: 159600 Effective search space used: 159600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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