Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_082109398.1 AL072_RS27445 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_001305595.1:WP_082109398.1 Length = 415 Score = 243 bits (621), Expect = 5e-69 Identities = 142/369 (38%), Positives = 206/369 (55%), Gaps = 26/369 (7%) Query: 16 LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75 LA+ + +M +DY G+ E T + N A ++ R R+ + ++ + +LG+ + + Sbjct: 17 LARRRVPRMFYDYVDCGSWTESTYRANTADLAALQFRQRIGMSIAGRTTESRILGESVAM 76 Query: 76 PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVA-EVGSKFSPSLQWF 134 P+ +AP + H +GE+ A AA G LST+S S+E+VA G F WF Sbjct: 77 PVALAPTGLTGMQHADGEILAARAAERFGVPFTLSTVSICSIEDVAANTGKPF-----WF 131 Query: 135 QLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTI 194 QLY+ +DR L+ RA AA AL LT+D + GQR +D +N PP L NL + Sbjct: 132 QLYVMRDRAFVERLIARAKAANCSALVLTLDLQIQGQRHKDLKNGLSTPPKPTLRNLVDL 191 Query: 195 S-----------------GLNIPHAPGES---GLFTYFAQQLNPALTWDDLEWLQSLSPL 234 + G + H G S L + +QQ +P LTW+D+ W++ L Sbjct: 192 ATKPGWCLGMLRTKRRTFGNIVGHVSGVSDVSSLAAWVSQQFDPTLTWEDVRWIKKLWGG 251 Query: 235 PLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLD 294 L++KG+L +DA AVE GA AIVVSNHGGRQLDGA +S+ LP I AV + EVL D Sbjct: 252 KLIVKGVLDVEDARLAVENGADAIVVSNHGGRQLDGAPSSIAMLPAIAEAVGQQTEVLFD 311 Query: 295 GGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQ 354 GIR G DI+KA A+GA+ V++GR L+GL G+AGV+ + +LQ+EL++ M L G + Sbjct: 312 SGIRSGQDILKAAALGAKGVMVGRAFLYGLGAMGEAGVTRCLEILQRELDLTMGLCGLTD 371 Query: 355 LQDIDTSFL 363 + D S L Sbjct: 372 IGAADPSIL 380 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: 341 Number of extensions: 15 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: 415 Length adjustment: 30 Effective length of query: 335 Effective length of database: 385 Effective search space: 128975 Effective search space used: 128975 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 24 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