Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate PP_5257 PP_5257 L-pipecolate oxidase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Putida:PP_5257 Length = 432 Score = 882 bits (2280), Expect = 0.0 Identities = 432/432 (100%), Positives = 432/432 (100%) Query: 1 MEPAMSELRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIV 60 MEPAMSELRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIV Sbjct: 1 MEPAMSELRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIV 60 Query: 61 LEAWKIGHGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLG 120 LEAWKIGHGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLG Sbjct: 61 LEAWKIGHGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLG 120 Query: 121 IDCQAQHKGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLD 180 IDCQAQHKGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLD Sbjct: 121 IDCQAQHKGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLD 180 Query: 181 RRAGTINPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVIST 240 RRAGTINPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVIST Sbjct: 181 RRAGTINPMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVIST 240 Query: 241 GAYTEGDWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGR 300 GAYTEGDWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGR Sbjct: 241 GAYTEGDWSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGR 300 Query: 301 LLLGSLGRVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAP 360 LLLGSLGRVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAP Sbjct: 301 LLLGSLGRVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAP 360 Query: 361 GLVAVTGYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFS 420 GLVAVTGYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFS Sbjct: 361 GLVAVTGYNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFS 420 Query: 421 LYHAGQCLRVVL 432 LYHAGQCLRVVL Sbjct: 421 LYHAGQCLRVVL 432 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: 856 Number of extensions: 22 Number of successful extensions: 1 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 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