Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_022949718.1 H035_RS0114640 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_000421465.1:WP_022949718.1 Length = 381 Score = 254 bits (648), Expect = 3e-72 Identities = 151/367 (41%), Positives = 208/367 (56%), Gaps = 24/367 (6%) Query: 9 NLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSV 68 N ++ +LA+ L FDY A DEIT + N A FER L P +L V ++L+ +V Sbjct: 8 NFHDFRELARRRLPGPIFDYIDGAADDEITHRRNSASFERCDLIPNVLRGVETVDLSATV 67 Query: 69 LGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFS 128 +GQ L LP+ +P A Q L H +GE A A AAA GT +S+L T SLEE+ + Sbjct: 68 MGQKLALPVYCSPTALQRLFHHQGERAVAAAAAKYGTMFGVSSLGTVSLEELRRTYA--- 124 Query: 129 PSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP----P 184 + Q +Q Y HKDRGL RA++ERA AAG + L LTVD+ G RERD R F +P P Sbjct: 125 -TPQVYQFYFHKDRGLNRAMLERAKAAGVEVLMLTVDSITGGNRERDLRTGFTIPFQLTP 183 Query: 185 GLHLA---------NLTTISGLNIPH-------APGESGLFTYFAQQLNPALTWDDLEWL 228 G L N +P + G + YF + L+P+L W D+E + Sbjct: 184 GGMLQFAIKPRWNWNYLMHEKFKLPQLEQHVDMSGGTLSIGRYFTEMLDPSLNWKDVEDM 243 Query: 229 QSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGK 288 P LKG+L DA RA E G I+VSNHGGRQLDG + D L E+V AV + Sbjct: 244 IRFWNGPFCLKGVLSAADARRAAEIGCTGIIVSNHGGRQLDGCRTAFDQLAEVVDAVGDR 303 Query: 289 AEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMA 348 +V++D G++RGT ++KAL++GA+AV +GR L+ LA GQAGV + L++ E+ M Sbjct: 304 VDVMMDSGVQRGTHVLKALSLGAKAVGLGRFYLFPLAAAGQAGVDRALGLMRAEIERGMK 363 Query: 349 LIGCSQL 355 L+GC+ + Sbjct: 364 LMGCTSI 370 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: 297 Number of extensions: 7 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: 381 Length adjustment: 30 Effective length of query: 335 Effective length of database: 351 Effective search space: 117585 Effective search space used: 117585 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