Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Ga0059261_2629 Ga0059261_2629 L-lactate dehydrogenase (FMN-dependent) and related alpha-hydroxy acid dehydrogenases
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Korea:Ga0059261_2629 Length = 379 Score = 251 bits (641), Expect = 2e-71 Identities = 146/373 (39%), Positives = 212/373 (56%), Gaps = 27/373 (7%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 ++E+ A+ + + FDY GA DE+TL N + I LR R+L DV+ ++L T++ G+ Sbjct: 8 DFEKAARRRVPRFLFDYAEGGAYDEVTLGRNVSDLAAIALRQRVLKDVANVDLKTTLFGR 67 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + LP+ + P+ + GE+ A AA +AG LST+S +LEEVA F Sbjct: 68 EVALPVALGPVGISGMYARRGEVQAARAAKAAGIPTCLSTVSICALEEVAAAADPF---- 123 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 WFQLY+ +DRG R L+ RA AAG +A+ TVD P+ G R R + P L + Sbjct: 124 -WFQLYVIRDRGFMRDLIARAKAAGAEAMVFTVDMPIPGARYRSEHSGMA-GPNARLRQI 181 Query: 192 TTISG----------LNIPHAPG--------ESGLFTYFA---QQLNPALTWDDLEWLQS 230 G + PH G +SGL Y + +P++ W DL+W+++ Sbjct: 182 LQAIGKPHWAWDVGLMGRPHTLGNLAPVLGKDSGLSDYMGWLGKNFDPSIQWKDLDWIRA 241 Query: 231 LSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAE 290 PL++KGIL +DA A GA IVVSNHGGRQLDG ++S ALP I AV G+ Sbjct: 242 EWDRPLIIKGILDPEDAREAAAIGANGIVVSNHGGRQLDGVLSSARALPPIADAVGGQLT 301 Query: 291 VLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALI 350 VL DGGIR G D+++ LA+GA VL+GR ++ LA G+AGV+ +++L+ +E+ VAM L Sbjct: 302 VLADGGIRTGLDVVRMLALGADGVLLGRAWVYALAAQGEAGVTKLLALIAREMKVAMTLT 361 Query: 351 GCSQLQDIDTSFL 363 G +++ ID S L Sbjct: 362 GVNRIGAIDRSIL 374 Lambda K H 0.320 0.136 0.391 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: 332 Number of extensions: 21 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: 365 Length of database: 379 Length adjustment: 30 Effective length of query: 335 Effective length of database: 349 Effective search space: 116915 Effective search space used: 116915 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: 49 (23.5 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