Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate Dsui_1668 Dsui_1668 alpha-hydroxyacid dehydrogenase, FMN-dependent L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__PS:Dsui_1668 Length = 374 Score = 301 bits (771), Expect = 2e-86 Identities = 163/353 (46%), Positives = 227/353 (64%), Gaps = 8/353 (2%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 +YE A+ L A+ Y SG+ DE+T + N+ F+R++L R+L DV + + GQ Sbjct: 20 DYEPYARRRLDDNAWTYLHSGSADELTFRWNKEAFDRLRLNGRVLADVRGGHTRLELFGQ 79 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + PL +AP+A Q L H EGELAT + A + GMV+STL++ LE++A + Sbjct: 80 RYEHPLFLAPVAHQKLFHPEGELATVLGAGALQAGMVVSTLASTPLEDIAAQAE----AP 135 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 WFQLY DR TR LV+RA AAGY+AL +TVD P+ G R R++R F LP G+ ANL Sbjct: 136 LWFQLYFQPDRDFTRQLVQRAEAAGYQALVVTVDVPIFGLRNREQRIGFHLPAGIDPANL 195 Query: 192 TTISGLNIPHA-PGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVLKGILRGDDAARA 250 ++ P PG+S +F + A TW+D+ W++SL+ LPL+LKGI DA +A Sbjct: 196 RGMAAPAQPALHPGQSIVFDGI---MAAAPTWEDIAWVRSLTRLPLILKGITHPGDARQA 252 Query: 251 VEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRGTDIIKALAIG 310 + G ++VSNHGGR LD AS++ALP +V AV G+ VLLDGGIRRG+D++KALA+G Sbjct: 253 ADLGVDGLIVSNHGGRSLDTLPASIEALPAVVQAVAGRLPVLLDGGIRRGSDVVKALALG 312 Query: 311 AQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDIDTSFL 363 A AVL+GRP ++GLA G GV+H + LL++EL V MA+ GC+ L DI+ L Sbjct: 313 AAAVLLGRPWVYGLAAAGPLGVAHTLKLLREELEVTMAMAGCTTLADINADLL 365 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: 326 Number of extensions: 12 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: 365 Length of database: 374 Length adjustment: 30 Effective length of query: 335 Effective length of database: 344 Effective search space: 115240 Effective search space used: 115240 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