Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate 15421 b1301 gamma-Glu-putrescine oxidase, FAD/NAD(P)-binding (NCBI)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Keio:15421 Length = 426 Score = 142 bits (357), Expect = 3e-38 Identities = 125/398 (31%), Positives = 185/398 (46%), Gaps = 17/398 (4%) Query: 34 DVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVG-LVNAGTWIRPDDV-EA 91 DVCV+GGG TGLS+A+HL E G V+VLEA +IG G SGRN G LVN ++ R DV E Sbjct: 29 DVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQLVN--SYSRDIDVIEK 86 Query: 92 TLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHEQWR 151 + G L ++ E + I+R IDC G L +A N +A LE + E W Sbjct: 87 SYGMDTARMLGSMMFEGGEIIRERIKRYQIDCD-YRPGGLFVAMNDKQLATLEEQKENWE 145 Query: 152 RRG-ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKIFQQS 210 R G +ELL + +D+ + ALLD G I+P+ G A A+ GG++++ S Sbjct: 146 RYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEADAIRLNGGRVYELS 205 Query: 211 SVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGD--WSNLQKQFFRGYYYQVASKPL 268 +V ++ V+TA+G V A+ V+++ AY GD L K+ + ++ L Sbjct: 206 AVTQIQHTTPA-VVRTAKGQVTAKYVIVAGNAYL-GDKVEPELAKRSMPCGTQVITTERL 263 Query: 269 QGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQSHY 328 A ++P D +L R RLL G + V Sbjct: 264 SEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGARDPDDVERLVVPKLLKT 323 Query: 329 YPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEFLL 388 +P+L V+ + WTG T + + + + GY+G G T + GR AE LL Sbjct: 324 FPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQGYSGHGVTCTHLAGRLIAE-LL 382 Query: 389 KGEADSLP----IPFSPMSGVSAPSLRTAFYESGFSLY 422 +G+A+ +P P G +LR F G + Y Sbjct: 383 RGDAERFDAFANLPHYPFPG--GRTLRVPFTAMGAAYY 418 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: 421 Number of extensions: 16 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: 426 Length adjustment: 32 Effective length of query: 400 Effective length of database: 394 Effective search space: 157600 Effective search space used: 157600 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