Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_011604951.1 FRAAL_RS16695 alpha-hydroxy-acid oxidizing enzyme
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_000058485.1:WP_011604951.1 Length = 402 Score = 236 bits (603), Expect = 6e-67 Identities = 145/357 (40%), Positives = 203/357 (56%), Gaps = 15/357 (4%) Query: 10 LFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVL 69 L E A+ L + +D+ GAG E TL+ NR F + RPR++ + T+VL Sbjct: 53 LTEIRAAAQAVLPRDVWDFLAGGAGQETTLRANRDAFGGWQFRPRVMSGHPVPSTATTVL 112 Query: 70 GQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSP 129 G P++LP+L AP T+G LA A A A GT ++ T S+E VA+ Sbjct: 113 GLPMRLPVLTAPFGTDGFFDTDGHLAVARANARCGTLSIVPEAGTHSIESVAQAAPA--- 169 Query: 130 SLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLA 189 + + QL+ G ++ER AGY A+C+TVD P G RER+ RN F + Sbjct: 170 AARVAQLHPMGTEGNFVRMLERIERAGYAAVCVTVDCPTAGWRERNLRNRFTV------- 222 Query: 190 NLTTISGLNIPHAPGESGLFTYFAQQL---NPALTWDDLEWLQSLSPLPLVLKGILRGDD 246 +L I+G N P G+ F Q P TWD L L + LP + KGIL D Sbjct: 223 DLRMITG-NYPPG-GDVAAQDVFGQLFARDEPVWTWDRLAGLMRHTDLPWIAKGILTAQD 280 Query: 247 AARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRGTDIIKA 306 A++ GA A++VSNHGGRQLDG A+LD LPE+VAA +G+AEVLLD G+R GTD++KA Sbjct: 281 TRAAIDAGAAAVLVSNHGGRQLDGTPAALDQLPEVVAAADGRAEVLLDSGVRCGTDVVKA 340 Query: 307 LAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDIDTSFL 363 LA+GA+AV+IGR GLA GG+AGV+ V++LL +E+ + L+G + ++ + L Sbjct: 341 LALGARAVVIGRLAAAGLAAGGEAGVARVLTLLHEEMVTVLTLLGHGSVTELTPAAL 397 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: 356 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: 402 Length adjustment: 30 Effective length of query: 335 Effective length of database: 372 Effective search space: 124620 Effective search space used: 124620 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