Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_011386798.1 AMB_RS22540 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_000009985.1:WP_011386798.1 Length = 384 Score = 202 bits (514), Expect = 1e-56 Identities = 131/379 (34%), Positives = 196/379 (51%), Gaps = 24/379 (6%) Query: 4 ISSPINLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQIN 63 I+ ++ + +LA+ + AF + G+G+E L+ NR E L P+ + Sbjct: 3 INHAASIGDLAKLARWRIPGFAFGFLDGGSGEEGGLRRNRERLEAAVLAPKACTGAKP-D 61 Query: 64 LTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEV 123 T S+ G+ LP AP+ L +L A AA G +V ST++T +LE++A Sbjct: 62 TTASLFGRDYALPFGAAPVGMGNLLWPGADLMVARQAARLGFPVVASTVATTALEDIAAA 121 Query: 124 GSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP 183 + WFQLY+ ++ + R L+ RA+AAG + L +TVD PV G R RD RN F+LP Sbjct: 122 AEGHA----WFQLYVSREERINRDLLARAWAAGIRELVITVDVPVAGDRRRDVRNRFILP 177 Query: 184 --PG------LHLANLTTISGL--------NIPHAPGE---SGLFTYFAQQLNPALTWDD 224 PG + +A L +S L N+ GE L + + Q+ L WDD Sbjct: 178 FKPGPRFVAQVAMAPLWALSTLRAGSPGFPNLTRYVGEVDGKTLAGFISSQIKDDLAWDD 237 Query: 225 LEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAA 284 + L+ L L++KGI+ DA A++ GA I VSNHGGRQLD A A++D+L I AA Sbjct: 238 VRALRDLWQGRLLIKGIMTAADARTALDLGADGIWVSNHGGRQLDAAPAAIDSLAAIRAA 297 Query: 285 VNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELN 344 + +A +L+DG IR G D+++A A GA V GR +G A G+ G + LL ++ Sbjct: 298 LGKEAVILMDGSIRSGEDVVRAGATGADFVFCGRAFYYGAAAAGEGGAARAADLLAADVR 357 Query: 345 VAMALIGCSQLQDIDTSFL 363 + IGC +D +L Sbjct: 358 RTLTQIGCPSWMGLDEGWL 376 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: 287 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: 384 Length adjustment: 30 Effective length of query: 335 Effective length of database: 354 Effective search space: 118590 Effective search space used: 118590 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 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