Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate 3608835 Dshi_2227 FAD dependent oxidoreductase (RefSeq)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Dino:3608835 Length = 434 Score = 145 bits (367), Expect = 2e-39 Identities = 122/395 (30%), Positives = 179/395 (45%), Gaps = 18/395 (4%) Query: 23 AAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGT 82 A A G DVC++GGG TGLSAA+HL E+G V+VLEA ++G G SGRN G V +G Sbjct: 27 ALPAAQGPIHTDVCIVGGGYTGLSAALHLAERGYDVVVLEAQRVGFGASGRNGGQVASGP 86 Query: 83 WIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIA- 141 + +EA G++ + EA V ++ R G+DC + G ++ A +A Sbjct: 87 RLDLSTLEARYGRETAHAQWALAREARKLVDELVAR-GLDCDLR-AGVIYATDRAGDVAG 144 Query: 142 -DLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVT 200 EA H Q V L + G+ + +LD A +NP+ GLA Sbjct: 145 YHAEAAHVQAAVGYDGVTPLDRDRIAALVGSAVYAGGVLDAGAAHLNPLKLVLGLADLAQ 204 Query: 201 RLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYY 260 G +IF+ S V + G V T + AE+V+++ Y G S Sbjct: 205 VAGAQIFEGSQVRSVADAGPHVVVTTDAATIAAEQVILAGNGYIGGLDSATAAHVMPINS 264 Query: 261 YQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGS----LGRVDNKPAWF 316 Y VA++PL G AD +LP G D + V++ RR GRLL G R A Sbjct: 265 YMVATEPL-GPDADAILPEGHAVADNKFVVNYFRRAPDGRLLFGGGESYRYRFTPDIAGK 323 Query: 317 VRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTG 376 VR +RI +P+L + + W G + T L + +P + + GY+G G Sbjct: 324 VRGPLERI----FPQLRGIGIDYAWGGTLAITRSRLPFARKVSPRVFSAGGYSGHGVALS 379 Query: 377 TVIGRAFAEFLLKGEADSL----PIPFSPMSGVSA 407 + G+A AE GE + +P +P G +A Sbjct: 380 LLFGKAMAE-AAAGEPERFNQLAALPHAPFPGGAA 413 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: 476 Number of extensions: 25 Number of successful extensions: 4 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: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 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