Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate WP_085636469.1 MGEO_RS08635 FAD-binding oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >NCBI__GCF_002115805.1:WP_085636469.1 Length = 434 Score = 141 bits (355), Expect = 5e-38 Identities = 114/384 (29%), Positives = 173/384 (45%), Gaps = 10/384 (2%) Query: 27 LAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRP 86 L GE +ADVC+IG G TGLSAA+HL E G V++L+A ++G G SGRN G + +G Sbjct: 31 LQGETRADVCIIGAGYTGLSAALHLAEMGADVVLLDAHRVGFGASGRNGGQLGSGQRQDQ 90 Query: 87 DDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLE-- 144 +E +G L + ++ V ++ R G+DC + G A DL Sbjct: 91 ITLEKLVGSDAARALWDLGEDSKTLVRDLVARHGLDCYLR-DGVAWAASRPADADDLHQY 149 Query: 145 ARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGG 204 A H Q R +E L C + LD AG ++P+ GLA A + G Sbjct: 150 AEHLQTRYGYDRIEALDRDAFHALCPSPDYIGGTLDMGAGHLHPLRLALGLADAAAKAGA 209 Query: 205 KIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVA 264 +I ++S V + R G V+T G V A++V+++ Y G + + Y VA Sbjct: 210 RIHERSHVHDI-RHGSKITVRTDAGHVIADQVILAGNGYLGGLDRQVIARVMPINNYIVA 268 Query: 265 SKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRI 324 ++PL G KVL D+R V++ R GRLL G + + + + Sbjct: 269 TEPL-GEDRMKVLTRDVAVADSRFVVNYFRLSHDGRLLFGGGETYGYRFPADIPALVRKR 327 Query: 325 QSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFA 384 + YP L V + W G + T + L P +++ +GY+G G T G+ A Sbjct: 328 MAVIYPHLRDVRIDYAWGGTLAITIRRMPYLARVRPNMLSASGYSGHGVGTAIQAGKLLA 387 Query: 385 EFLLKGEADSL----PIPFSPMSG 404 E +G +D IP +P G Sbjct: 388 E-ATRGTSDGFETYNAIPHTPFPG 410 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: 486 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: 434 Length adjustment: 32 Effective length of query: 400 Effective length of database: 402 Effective search space: 160800 Effective search space used: 160800 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 24 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