Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate GFF3817 PGA1_262p02210 FAD dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Phaeo:GFF3817 Length = 433 Score = 299 bits (766), Expect = 1e-85 Identities = 167/419 (39%), Positives = 229/419 (54%), Gaps = 1/419 (0%) Query: 5 MSELRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAW 64 M+ R + LW+ + + A AL + AD+ V+GGG TG SAA+ E G V +LEA Sbjct: 1 MTPDRNRSLWQATCREDLDAAALHDDVSADLVVVGGGYTGCSAALRAAELGADVRLLEAE 60 Query: 65 KIGHGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQ 124 G GGSGRNVGLVNAG W+ P + + LG+ G+RL+ +L APA VF +I+ IDC+ Sbjct: 61 TFGAGGSGRNVGLVNAGLWLPPKKINSVLGEVNGTRLSTLLAAAPAAVFELIKTHQIDCE 120 Query: 125 AQHKGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAG 184 GTLH AH +G+ DL RH+Q GA V LL+ G+D + AL D RAG Sbjct: 121 PIQTGTLHCAHARSGLKDLRKRHQQLTAIGAPVTLLSRGDAIARVGSDAVYGALFDPRAG 180 Query: 185 TINPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYT 244 TI P+ Y GLA A G ++ S V GL RE DGWRV T G VRA ++++T AY Sbjct: 181 TIQPLAYAIGLARAAASQGARLHASSPVVGLTRETDGWRVSTPGGTVRARHLIMATNAYP 240 Query: 245 EGDWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLG 304 Y+Q A+ PL A ++LP +G WDT ++SS RRD GRL++G Sbjct: 241 LPITGYTAPATIPVSYFQAATAPLPAGLAGRILPQAEGCWDTGLIMSSWRRDRAGRLIIG 300 Query: 305 SLGRVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVA 364 +G + + +W R + +P L +E W G I T +H+ ++ + G A Sbjct: 301 GMGDLSHPARSVHTNWLRRKLAVMFPALADHPFEAEWAGKIAMTTEHIPKIIDLGQGF-A 359 Query: 365 VTGYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYH 423 GY+GRG GTV GR AE L+ G+ LPIP S + +R +YE+G +L H Sbjct: 360 CFGYSGRGIGPGTVFGRRMAEALMHGDRSLLPIPVSDDHRLPFAGVRGTYYETGATLVH 418 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: 533 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: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 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