Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate H281DRAFT_02574 H281DRAFT_02574 Glycine/D-amino acid oxidase (deaminating)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Burk376:H281DRAFT_02574 Length = 431 Score = 254 bits (648), Expect = 5e-72 Identities = 147/411 (35%), Positives = 211/411 (51%), Gaps = 1/411 (0%) Query: 13 LWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSG 72 LW ++P L DV ++G G TGLS A+HL E+G V VL+A + G G SG Sbjct: 14 LWAATAQPAPDTPPLRESASFDVAIVGAGFTGLSTALHLAERGVKVCVLDAAEPGWGASG 73 Query: 73 RNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLH 132 RN G V G PD++ G+ G+RL +V+G A VF +I+R GI+C A G + Sbjct: 74 RNGGQVIPGLKYDPDELVQRFGETAGNRLVEVVGGAADNVFDLIDRYGIECSAVRSGWIQ 133 Query: 133 MAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYT 192 A + + + R QW RGA V LL GA+ GT +D RAG+I P+ Y Sbjct: 134 PAPSRAMLEAVTRRARQWEARGAKVSLLDGAEVSRRLGTKSYIGGWIDHRAGSIQPLSYV 193 Query: 193 QGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGA-VRAEKVVISTGAYTEGDWSNL 251 +GLA A LG + +++V L R GWRV+T GA V A++VV++T YT W L Sbjct: 194 RGLARAAQSLGVAVHGRTAVSRLMRNERGWRVETQGGASVEAQRVVVATNGYTGALWPGL 253 Query: 252 QKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDN 311 ++ + VA++PL D +L G+ + D+R +L RRD GRLL+G G Sbjct: 254 RQSVIAANSFIVATRPLPTGIGDDILRGGEVASDSRRLLLYFRRDAAGRLLMGGRGPFSE 313 Query: 312 KPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGR 371 A + +R YP+L + +E W G + T D L + EPAPGL GYNGR Sbjct: 314 PSANGDWAHLERAVELMYPQLKGIGYEYRWAGRVAITADFLPHVHEPAPGLSIALGYNGR 373 Query: 372 GNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLY 422 G T +G+ AE + G A + P +P+ + L+ + +G + Y Sbjct: 374 GIAMATTVGKHLAERMCSGSAAAFPFAVTPVRSIPFHGLQRFYITAGVAWY 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: 502 Number of extensions: 22 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: 431 Length adjustment: 32 Effective length of query: 400 Effective length of database: 399 Effective search space: 159600 Effective search space used: 159600 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