Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_068174554.1 HTA01S_RS20150 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_001592305.1:WP_068174554.1 Length = 383 Score = 259 bits (662), Expect = 8e-74 Identities = 151/384 (39%), Positives = 225/384 (58%), Gaps = 29/384 (7%) Query: 1 MTAISSPINLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVS 60 MT I+ N+ + LA+ + +M +DY SG+ E T + N + F++IKLR R+ V++ Sbjct: 1 MTVIT---NIEDLRVLAEKRVPRMFYDYADSGSWTESTYRANASDFQKIKLRQRVAVNME 57 Query: 61 QINLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEV 120 + ++++GQ + +P+ IAP + H +GE+ A AA G LST+S S+E+V Sbjct: 58 NRSTASTMVGQEVFMPVAIAPTGLTGMQHADGEILAARAARRFGIPFTLSTMSICSIEDV 117 Query: 121 AE-VGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNE 179 A+ G F WFQLY+ KDR L++RA AA AL LT+D +LGQR +D +N Sbjct: 118 AQHAGQGF-----WFQLYVMKDRAYIERLIDRAKAANCSALVLTLDLQILGQRHKDLKNG 172 Query: 180 FVLPPGLHLANLTTIS-----------------GLNIPHAPGESG---LFTYFAQQLNPA 219 PP L +AN+ + G I H G L + A+Q +PA Sbjct: 173 LSAPPKLTVANILNMMTKPRWGLGMLGTKRHGFGNIIGHVSGVDNMGSLSEWTAKQFDPA 232 Query: 220 LTWDDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALP 279 L W D+EW++ L+LKGI +DA AV GA A++VSNHGGRQLDGA +S++ALP Sbjct: 233 LNWGDVEWIKQRWGGKLILKGIQDVEDAKLAVASGADALIVSNHGGRQLDGAQSSIEALP 292 Query: 280 EIVAAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLL 339 +V AV + EV +DGGIR G D++KA A+GA+ V IGRP L+GL G+AGV+ + ++ Sbjct: 293 AVVDAVGSQIEVHMDGGIRSGQDVLKARALGARGVYIGRPFLYGLGAMGEAGVTKCLEII 352 Query: 340 QKELNVAMALIGCSQLQDIDTSFL 363 +EL++ MA G ++++ +D L Sbjct: 353 HRELDLTMAFCGHTKIETVDKGIL 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: 337 Number of extensions: 12 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: 383 Length adjustment: 30 Effective length of query: 335 Effective length of database: 353 Effective search space: 118255 Effective search space used: 118255 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