Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate 6938535 Sama_2638 putative oxidoreductase (RefSeq)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__SB2B:6938535 Length = 428 Score = 142 bits (359), Expect = 2e-38 Identities = 122/400 (30%), Positives = 182/400 (45%), Gaps = 12/400 (3%) Query: 30 EH-KADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRPDD 88 EH + DVCVIG G TGLS+A+HLLE G V+VLEA +IG G SGRN G + D Sbjct: 26 EHLETDVCVIGAGYTGLSSALHLLESGFKVVVLEAARIGWGASGRNGGQIVNSYSRDIDV 85 Query: 89 VEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHE 148 +E T+G+++G ++ E + I + IDC ++ G + A N + L+A+ Sbjct: 86 IEKTVGKEKGKLFGEMAFEGGRIIRDRIAKYNIDCDLKN-GGVFAALNQKQMGHLKAQKA 144 Query: 149 QWRRRG--ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKI 206 W G +E+L A + T++ +LD+ G I+P+ G A AV LGGKI Sbjct: 145 LWEAHGHTNQLEILDEAGIRNVVNTERYVGGMLDKSGGHIHPLNLALGEARAVESLGGKI 204 Query: 207 FQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQVASK 266 F+ S+V + EG+ VKT G V+A VV++ AY L + + ++ Sbjct: 205 FEDSAVLDVV-EGEPAIVKTEFGQVKARFVVVAGNAYLGKLMPELMAKSMPCGTQVITTE 263 Query: 267 PLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQS 326 PL A+ +LP D +L R RL+ G + ++S Sbjct: 264 PLSDEMANSLLPQDYCVEDCNYLLDYFRLSGDKRLIYGGGVVYGARDPDNIKSIILPKML 323 Query: 327 HYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEF 386 +P+L V + WTG T L ++ + G +G G T + G+ AE Sbjct: 324 ETFPQLKGVRIDYTWTGNFLLTLSRLPQVGRIGKNIYYSQGCSGHGVTYTHLAGKLIAE- 382 Query: 387 LLKGEADSLPI----PFSPMSGVSAPSLRTAFYESGFSLY 422 +L G+A + P P G A LR F G Y Sbjct: 383 VLNGQATRFDVFAELPHYPFPGGHA--LRVPFSAIGAWYY 420 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: 441 Number of extensions: 22 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: 428 Length adjustment: 32 Effective length of query: 400 Effective length of database: 396 Effective search space: 158400 Effective search space used: 158400 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