Align (S)-2-hydroxy-acid oxidase (EC 1.1.3.15); L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate SMc01740 SMc01740 L-lactate dehydrogenase (cytochrome) protein
Query= BRENDA::A9QH69 (390 letters) >FitnessBrowser__Smeli:SMc01740 Length = 364 Score = 154 bits (389), Expect = 4e-42 Identities = 111/342 (32%), Positives = 155/342 (45%), Gaps = 16/342 (4%) Query: 25 DFVNVFDLEKMAQKVIPKGAFGYIASGAGDTFTLHENIRSFNHKLIVPHGLKGVENPSTE 84 DF ++ ++ + AQ +PK + + GA TL N + + P L+ V Sbjct: 15 DFESLQEIIQKAQGALPKEKWDSLVGGAETETTLKRNRLAIDSIAFKPRVLRNVSVVDLS 74 Query: 85 ITFDGDKLASPIILAPVAAHKLANEQGEIASAKGVKEFGTIYTTSSYSTTDLPEISQTLG 144 I G +L PI LAP L G A A G + FG + SS T L +++ Sbjct: 75 IEHFGRRLRLPIFLAPTGPLNLFGPGGGAAVASGAQVFGVAHMLSS-GCTPLESVAEAAP 133 Query: 145 DSPHWFQFYYSKDDGINRHIMDRLKAEGVKSIVLTVDATVGGNREVDKRNGFVFPVGMPI 204 + Q Y DD + R A G +I LTVD+ V R+ D I Sbjct: 134 SALRMAQLYVRGDDASVHKYVGRALASGCAAICLTVDSAVLARRDRD------------I 181 Query: 205 VQEYLPNGAGKTMDYVYKATKQALSPKDVEYIAQYSGLPVYVKGPQCAEDAFRALEAGAS 264 + G GK Y+A L + V+ I +P+ +KG EDA A++ G Sbjct: 182 ANRHRTAGLGKWPGQAYQA---GLDWRTVKLIKDSYDIPLVLKGIATVEDARIAVDHGVD 238 Query: 265 GIWVTNHGGRQLDGGPAAFDSLQEVAEAVDRRVPIVFDSGVRRGQHVFKALASGADLVAL 324 I+V+NHGGRQLD G D L E+ +AV + ++ D G RG + KALA GA+LV L Sbjct: 239 WIYVSNHGGRQLDHGRGTMDVLPEIIDAVGGQAKVMVDGGFCRGTDIIKALAIGANLVGL 298 Query: 325 GRPVIYGLAMGGSVGTRQVFEKINDELKMVMQLAGTQTIDDV 366 GR Y LA GG ++ E I DE+ M L G TI D+ Sbjct: 299 GRMQCYALAAGGEAAIIRMLELIEDEMLRSMALLGVPTIGDL 340 Lambda K H 0.316 0.135 0.388 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: 361 Number of extensions: 18 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: 390 Length of database: 364 Length adjustment: 30 Effective length of query: 360 Effective length of database: 334 Effective search space: 120240 Effective search space used: 120240 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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