Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate H281DRAFT_06337 H281DRAFT_06337 Glycine/D-amino acid oxidase (deaminating)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Burk376:H281DRAFT_06337 Length = 424 Score = 156 bits (395), Expect = 1e-42 Identities = 119/396 (30%), Positives = 187/396 (47%), Gaps = 12/396 (3%) Query: 8 LRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIG 67 ++ + W + P V A + ADV VIG G TGLSAA+ L ++G SV V++A ++G Sbjct: 1 MKLESYWLDTAPPFVTACEGPVDGLADVVVIGAGFTGLSAALALGKRGASVTVVDAGRVG 60 Query: 68 HGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQH 127 G SGRN G VN G + A LG ++ S + +A V +I IDC Sbjct: 61 GGASGRNGGQVNTGVAQDFVALAAQLGIERASACYRAFADAVDTVERLIREEQIDCDYLA 120 Query: 128 KGTLHMAHNATGIADLEARHEQWRRR-GADVELLTGAQCQEYCGTDKISAALLDRRAGTI 186 G L +A +A LE + RR D+EL+ G + + +D LL R G + Sbjct: 121 SGKLKLASKPHHLAHLEKTADLIRRTVDTDIELIDGDRIRSEVQSDSFHGGLLQRHGGQM 180 Query: 187 NPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEG 246 + +T GLA A R G K+++ ++V + ++G RV T RG VRA++V+I+TG G Sbjct: 181 HMGKFTVGLAEAAVRRGAKLYENAAVTSIVKDGGAHRVVTTRGEVRAKQVLIATGPSRHG 240 Query: 247 DWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSL 306 + +++ + V ++PL KVLP+ + TR + + R RLL G Sbjct: 241 PFGWYRRRLAPVGSFIVVTEPLPPELLAKVLPNRRAYTTTRLMHNYFRVTPDSRLLFGGR 300 Query: 307 GR--VDNKPAWFVRSWADRIQSH----YYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAP 360 R +P+ + + RI +P L + W G +D + D L + Sbjct: 301 ARFTASERPS---DAKSGRILQQGLAVMFPMLSSARIDYCWGGLVDISADRLPHAGQ-HD 356 Query: 361 GLVAVTGYNGRGNTTGTVIGRAFAEFLLKGEADSLP 396 G+ GY+G G T +G+ A+ ++ G D P Sbjct: 357 GIYFSMGYSGHGTQMSTHMGQVMAD-VMDGREDRNP 391 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: 498 Number of extensions: 21 Number of successful extensions: 2 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: 424 Length adjustment: 32 Effective length of query: 400 Effective length of database: 392 Effective search space: 156800 Effective search space used: 156800 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