Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate AO353_24430 AO353_24430 amino acid oxidase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24430 Length = 434 Score = 224 bits (572), Expect = 3e-63 Identities = 130/411 (31%), Positives = 198/411 (48%), Gaps = 4/411 (0%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 +W + LA + DV +IGGG G++A +H E+G I++EA +IG G SG Sbjct: 20 MWSATGGEKPESVVLARQESCDVLIIGGGFNGVTAGLHCAERGARTILVEAQEIGSGASG 79 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G VN G ++ P+ + LG G K LG AP V +I GIDC A + + Sbjct: 80 RNAGQVNPGQFLSPEQILRALGPDYGQLFLKELGSAPDVVRQLIRDYGIDCAADERPIIR 139 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 + + +LE + W+ GA+V+++ G++ +E G+ + AAL+D R T+ P+ Y Sbjct: 140 CSTSPQKTRELEIQASDWQALGANVQMVYGSELEEMNGSIRYKAALIDHRGFTLQPLAYV 199 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQ 252 +GLA A G +I S V LE G GW T ++A+KV++ST AY+ + Sbjct: 200 RGLARAAVARGLRISTGSKVTSLEPSGTGWVATTGNTTIKADKVILSTNAYSNDLVPGFK 259 Query: 253 KQFF-RGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311 ++ G + + PL +++LPH WDT + R D GRL +GS+G + Sbjct: 260 EEIMPLGAFGIATADPLPPEWRERILPHYIAMWDTHKIPLWFRYDPVGRLHVGSIGFLPI 319 Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371 +W +R YP +W W+G + T D L L EP PG+ A G NGR Sbjct: 320 HSEG--DNWVNRAMKFVYPFAPTFKWGYRWSGTLGQTVDRLPHLVEPRPGIFATIGCNGR 377 Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422 G G+ A+ L G+ P+P S + Y++G Y Sbjct: 378 GIAPNAYFGKMLAKIAL-GDDVITPLPLRTSSKYPMREIALEAYDAGIRFY 427 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: 468 Number of extensions: 20 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: 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