Align Lactate 2-monooxygenase; EC 1.13.12.4; Lactate oxidase (uncharacterized)
to candidate CCNA_01462 CCNA_01462 lactate 2-monooxygenase
Query= curated2:P21795 (394 letters) >FitnessBrowser__Caulo:CCNA_01462 Length = 391 Score = 473 bits (1218), Expect = e-138 Identities = 230/394 (58%), Positives = 290/394 (73%), Gaps = 7/394 (1%) Query: 1 MSNWGDYENEIYGQGLVGVAPTLPMSYADWEAHAQQALPPGVLSYVAGGSGDEHTQRANV 60 M+++GDY+NEIYG GL GV P P+ + EA A A+ P +LSYV GG GDE TQR N Sbjct: 1 MAHYGDYQNEIYGAGLQGVRPKWPVDFKTLEARATAAMSPDLLSYVQGGCGDEFTQRRNA 60 Query: 61 EAFKHWGLMPRMLMAATERDLSVELWGKTWAAPMFFAPIGVIALCAQDGHGDAASAQASA 120 +AF WG++PRM++ A++RDLS+EL+G P+F +PIGVI +CAQDGHGD A+A A+ Sbjct: 61 DAFHDWGVVPRMMVDASKRDLSIELFGLKLPTPLFMSPIGVIGMCAQDGHGDIATAVAAQ 120 Query: 121 RTGVPYITSTLAVSSLEDIRKHAGDTPAYFQLYYPEDRDLAESFIRRAEEAGYDGLVITL 180 RTGVP + STLA +E + GD +FQLY P+DRDLAES IRRAE AG+ LV+TL Sbjct: 121 RTGVPVMASTLANDPIEKVGAALGDGVGFFQLYTPKDRDLAESLIRRAETAGFKALVVTL 180 Query: 181 DTWIFGWRPRDLTISNFPFLRGLCLTNYVTDPVFQKKFKAHSGVEAEGLRDNPRLAADFW 240 DTW+ GWRPRDL +NFP LRG L NY TDP F + + + + ++P A W Sbjct: 181 DTWVTGWRPRDLNDANFPQLRGHVLQNYFTDPRFLE-------ILGKPVAEDPATAIRTW 233 Query: 241 HGLFGHSVTWEDIDWVRSITKMPVILKGIQHPDDARRAVDSGVDGIYCSNHGGRQANGGL 300 GLFG ++TWED+ W+RS TK+P++LKGI HPDDARRAVD GVDG++CSNHGGRQANGG+ Sbjct: 234 GGLFGKTLTWEDLAWLRSATKLPIVLKGICHPDDARRAVDLGVDGVFCSNHGGRQANGGI 293 Query: 301 PALDCLPEVVKASGDTPVLFDSGIRTGADVVKALAMGASAVGIGRPYAWGAALGGSKGIE 360 A+D L +VV ASG+TPVLFDSG+R+G+D KALAMGA AVGIGRPYA+G A+GG G+ Sbjct: 294 AAIDLLEDVVTASGNTPVLFDSGVRSGSDAAKALAMGARAVGIGRPYAYGLAIGGVDGVV 353 Query: 361 HVARSLLAEADLIMAVDGYRNLKELTIDALRPTR 394 HV RS+LAE DL+MAVDG+ L L +RP R Sbjct: 354 HVLRSILAELDLLMAVDGFPTLAALRDAGVRPVR 387 Lambda K H 0.319 0.137 0.430 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: 557 Number of extensions: 19 Number of successful extensions: 3 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: 394 Length of database: 391 Length adjustment: 31 Effective length of query: 363 Effective length of database: 360 Effective search space: 130680 Effective search space used: 130680 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 (21.8 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