Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate GFF3028 PS417_15495 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__WCS417:GFF3028 Length = 422 Score = 243 bits (619), Expect = 1e-68 Identities = 142/420 (33%), Positives = 217/420 (51%), Gaps = 2/420 (0%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW + V AL K DV ++G G TGLS A+HL E+G SV VLEA + G G SG Sbjct: 4 LWSATAPSVVPTPALRESVKVDVAIVGAGYTGLSTALHLAERGVSVCVLEANEPGWGASG 63 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G VN P+ + G ++ L + + VF +IE+ GIDC KG + Sbjct: 64 RNGGQVNPTLKYDPEQLVQMFGPERAEPLISTVSSSADLVFKLIEKHGIDCAPVRKGWMQ 123 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 +++ G+A L AR +QW RRG V+ L + G+D + LD RAG I P+ Y Sbjct: 124 VSYTEKGVAGLHARADQWARRGVPVQRLDASTVASRMGSDAFAGGWLDGRAGAIQPLAYA 183 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGA-VRAEKVVISTGAYTEGDWSNL 251 +GL A G +I QS+V L R+G GW+++TA GA V A++VV++T Y+ W + Sbjct: 184 RGLVGAALAAGVRIHGQSAVTDLRRQGAGWQLQTASGARVMADQVVLATNGYSGNLWPGM 243 Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311 + + VA+ PL G A+++LP + + +L R+D GRLL+G G ++ Sbjct: 244 AQSVLAANSFIVATTPLSGSVAERILPGQETVSTAQRLLLYFRKDSHGRLLMGGRGLFND 303 Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371 + + +R + +P+LG +++E W G I T D + + +PAPGL G NGR Sbjct: 304 PTSPTDFAHLERSLALLFPQLGPLQFEYRWAGRIAITRDFMPHVHQPAPGLTLALGCNGR 363 Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYHAGQCLRVV 431 G T +G+ A L +A+ P +P+ + L+ + +G + Y L +V Sbjct: 364 GIALCTSLGQQLAGKLCDSQAE-FAYPVTPLQRLPMHGLQRFYIGAGVAWYSLLDRLNIV 422 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: 457 Number of extensions: 15 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: 422 Length adjustment: 32 Effective length of query: 400 Effective length of database: 390 Effective search space: 156000 Effective search space used: 156000 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