Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate AO353_27485 AO353_27485 FAD-dependent oxidoreductase
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27485 Length = 429 Score = 155 bits (391), Expect = 3e-42 Identities = 125/383 (32%), Positives = 178/383 (46%), Gaps = 25/383 (6%) Query: 27 LAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVNAGTWIRP 86 L GEH A+V +IG G +GL A+ L GK V +LEA ++ SGRN G G Sbjct: 27 LEGEHTAEVLIIGAGFSGLHTALRLALAGKRVTLLEASRVAWAASGRNGGQAILGWSCDM 86 Query: 87 DDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQ--HKGTLHMAHNATGIADL- 143 +E LG ++ RL + A E+ + R G DC + H T M + + + Sbjct: 87 PPLETALGYERARRLWDGMRWAAQELRGLPARHGFDCDYRPGHLWTSVMPRRVSLLTEWQ 146 Query: 144 -EARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRL 202 EA H+ W G ++ +T Q ++ +++ A L D G +NP+ GLAAA+ R Sbjct: 147 REASHK-WGHDG--LQFITREQLPQWVASERYQAGLYDPEGGHLNPLKLALGLAAAIERA 203 Query: 203 GGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFRGYYYQ 262 GG IF+QS EGD +RV T RG++RA +V++ AY + L YQ Sbjct: 204 GGCIFEQSKALSYREEGDQYRVTTERGSIRANVLVLACNAYLDQLDPELASCVLPVGTYQ 263 Query: 263 VASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGS----LGRVDNKPAWFVR 318 VA+ PL A +LP D + VL RR RLL G LG + A R Sbjct: 264 VATAPLTAEQASALLPSNVCVTDNQFVLDYFRRTPDNRLLFGGGCTYLGGMPKDIAAATR 323 Query: 319 SWADRIQSHYYPELGKVEWEMHWTGCIDF----TPDHLMRLFEPAPGLVAVTGYNGRGNT 374 + +R+ +P+L VE E W G ID TPD R L + GY+G G Sbjct: 324 PYLERV----FPQLKGVELEFAWGGHIDLTLKRTPDIGRR-----GDLYWLQGYSGHGVL 374 Query: 375 TGTVIGRAFAEFLLKGEADSLPI 397 RA ++ +L G+ D L + Sbjct: 375 PTLAGARAVSDAIL-GQPDELAL 396 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: 489 Number of extensions: 30 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: 429 Length adjustment: 32 Effective length of query: 400 Effective length of database: 397 Effective search space: 158800 Effective search space used: 158800 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