Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate PfGW456L13_3923 Nucleoside-diphosphate-sugar epimerases
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3923 Length = 400 Score = 139 bits (349), Expect = 2e-37 Identities = 118/396 (29%), Positives = 175/396 (44%), Gaps = 10/396 (2%) Query: 32 KADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRPDDVEA 91 + DVCVIG G TGLSAA+ LLE G V VLEA ++G G SGRN G + D +E Sbjct: 2 ETDVCVIGAGYTGLSAALFLLENGFKVTVLEAARVGFGASGRNGGQIVNSYSRDIDVIER 61 Query: 92 TLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHEQWR 151 T+G KQ L ++ E + + R I C + G + A A + LE++ W Sbjct: 62 TVGPKQAQLLGQMAFEGGRIIRERVARYNIQCDLK-DGGVFAAMTAKQMGHLESQKRLWE 120 Query: 152 RRG-ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKIFQQS 210 R G +EL+ + +E D+ +LD G I+P+ G AAAV LGG I++QS Sbjct: 121 RFGHTQLELMDQRRIREVVACDQYVGGMLDMSGGHIHPLNLALGEAAAVESLGGTIYEQS 180 Query: 211 SVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVASKPLQG 270 +ER G V T +G VRA+ ++++ AY L + + ++PL Sbjct: 181 PAVRIER-GASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVITTEPLGE 239 Query: 271 IAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQSHYYP 330 A +LP D +L R RL+ G + + + +P Sbjct: 240 ELAKTLLPQDYCVEDCNYLLDYYRLSGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFP 299 Query: 331 ELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEFLLKG 390 +L V+ + WTG T L ++ + G +G G T + G+ AE L+G Sbjct: 300 QLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAE-ALRG 358 Query: 391 EADSL----PIPFSPMSGVSAPSLRTAFYESGFSLY 422 +A+ +P P G LRT F G Y Sbjct: 359 QAERFDAFADLPHYPFPG--GQLLRTPFAALGAWYY 392 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: 420 Number of extensions: 26 Number of successful extensions: 5 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: 400 Length adjustment: 31 Effective length of query: 401 Effective length of database: 369 Effective search space: 147969 Effective search space used: 147969 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: 50 (23.9 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