Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate SMc01576 SMc01576 oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Smeli:SMc01576 Length = 429 Score = 325 bits (834), Expect = 1e-93 Identities = 170/415 (40%), Positives = 247/415 (59%), Gaps = 5/415 (1%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW + LAG+ +V ++GGG TGLSAA+HL E G V+EA IG GGSG Sbjct: 10 LWHATAPAAPRTAPLAGDLTVEVAIVGGGFTGLSAALHLAETGIRTAVIEARMIGFGGSG 69 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RNVGLVNAG W++PDD+ ATLG G+RL LG+ P+ V+ ++ + GI+C+A GTLH Sbjct: 70 RNVGLVNAGMWVQPDDLIATLGAAAGNRLLDELGDGPSFVYDLVAKHGIECEAVRNGTLH 129 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 M+ A G+ ++ R QW++RGA VE+L+ + G + + ALLDRRAGTI P+ Y Sbjct: 130 MSVGAEGLKEIREREAQWKKRGAPVEVLSAEKAHALSGAEGFTGALLDRRAGTIQPLAYA 189 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAY----TEGDW 248 +GLA A G +IF + + R+GD W +KT RG V A V+++T AY T W Sbjct: 190 RGLARAALAAGAEIFTDTPLLAASRQGDLWNLKTPRGTVTARHVILATNAYGSLVTGVPW 249 Query: 249 SNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGR 308 +++ Y+Q A+ PL A ++LP QG+WDT V++S R D Q RL+ GS+GR Sbjct: 250 KEYRQELTILPYFQFATNPLPDNVAARILPERQGAWDTGLVMTSFRMDRQNRLIFGSIGR 309 Query: 309 VDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGY 368 +D A R++A R +P +G +E W G I T ++L + AP +V+++GY Sbjct: 310 LDAIAAGTHRAFAARSVRKLFPYIGDFRFEHWWDGRIGMTTNNLPAMHVLAPNVVSISGY 369 Query: 369 NGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYH 423 NGRG GTV GRA A + G+ ++P+ +P++ +L++AFY +G H Sbjct: 370 NGRGIAPGTVFGRALARH-VTGDTSAIPLAETPVTPDPWRTLKSAFYHAGAQAKH 423 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: 512 Number of extensions: 24 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: 429 Length adjustment: 32 Effective length of query: 400 Effective length of database: 397 Effective search space: 158800 Effective search space used: 158800 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