Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate WP_013518247.1 ALIDE2_RS17665 FAD-binding oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >NCBI__GCF_000204645.1:WP_013518247.1 Length = 432 Score = 238 bits (608), Expect = 2e-67 Identities = 143/411 (34%), Positives = 203/411 (49%), Gaps = 2/411 (0%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW + AL DV V+G G TGLS A+HL E G V VL+A G G SG Sbjct: 15 LWAATAPAAPDTPALGASVSTDVLVVGAGYTGLSTALHLAESGARVCVLDAHAPGWGASG 74 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G VN PDD+ G ++ L + + V+ +I R IDC G L Sbjct: 75 RNGGQVNPTLKYDPDDLVRIYGAERAEPLIDTVSRSADLVYGLIARHAIDCAPVRAGWLQ 134 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 + + + + AR QW RRG VE+L A GT + LD RAG + P+ Y Sbjct: 135 VGYTQHAVDGMHARARQWERRGVRVEMLDRAAVAARIGTPAFAGGWLDGRAGGVQPLAYA 194 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARG-AVRAEKVVISTGAYTEGDWSNL 251 +GLA A LG ++ S V LER+G W TA+G V+A++VV+ T YT+G W L Sbjct: 195 RGLARAAQGLGVQVHGGSPVVALERQGMHWIATTAQGHRVQAQQVVLGTNGYTDGLWPGL 254 Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311 + + VA++PL G A D +LP G+ ++ +L R+D QGRLL+G G + Sbjct: 255 ARTVLAANSFIVATRPL-GPAGDGILPGGETGSTSQRLLLYFRKDAQGRLLMGGRGHFAD 313 Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371 S +R + +P+LG +++E W G I T D + L PAPG+ GYNGR Sbjct: 314 PQGPQDFSHLERAVALMFPQLGPLQYEYRWAGRIAVTRDFMPHLHRPAPGITMALGYNGR 373 Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422 G T +GR A + A + P P +P+ + L+ + +G + Y Sbjct: 374 GIAMATSLGRHAAALVAGSSAAACPFPVTPVQPIPLHGLQRFYIAAGVAWY 424 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: 514 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: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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 Apr 09 2024. 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