Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_057508630.1 ABB28_RS10775 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_001431535.1:WP_057508630.1 Length = 379 Score = 242 bits (617), Expect = 1e-68 Identities = 146/372 (39%), Positives = 208/372 (55%), Gaps = 24/372 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 +Y A+ L F Y GA E TL+ N I LR R+L D+S+++L T + G+ Sbjct: 8 DYRAAAQRRLPPFLFHYVDGGAYAEHTLRRNVEDLAGIALRQRVLRDMSELDLQTELFGE 67 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 L +P+ +AP+ + GE+ A AAAS G LST+S +EEVA ++ Sbjct: 68 TLAMPVALAPVGLTGMFARRGEVQAARAAASRGIPFTLSTVSVCPIEEVAPAINR----P 123 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP------PG 185 WFQLY+ +DRG R +ERA AAG L TVD PV G R RD + P G Sbjct: 124 MWFQLYVLRDRGFMRDALERAQAAGVTTLVFTVDMPVPGARYRDMHSGMSGPNAALRRAG 183 Query: 186 LHLANLTTISGLNI---PHAPGE--------SGLFTYFA---QQLNPALTWDDLEWLQSL 231 LA+ + + PH G +GL Y +P+++W DLEW+++ Sbjct: 184 QVLAHPRWAWDVGLRGRPHDLGNISAYRGNPTGLADYIGWLGSNFDPSISWKDLEWIRAF 243 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 P+++KGIL DDA A+ +GA IVVSNHGGRQLDG +++ ALP I AV G+ ++ Sbjct: 244 WKGPMIIKGILDADDARDALRFGADGIVVSNHGGRQLDGVLSTARALPAIADAVKGELKI 303 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 L D GIR G D+++ LA+GA AVL+GR ++ LA G+AGV++++ L+ KE+ VAM L G Sbjct: 304 LADSGIRSGLDVVRMLALGADAVLLGRAFVYALATHGEAGVANLLDLVAKEMRVAMTLTG 363 Query: 352 CSQLQDIDTSFL 363 ++ DI L Sbjct: 364 ARRIADIGPGLL 375 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: 311 Number of extensions: 19 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: 379 Length adjustment: 30 Effective length of query: 335 Effective length of database: 349 Effective search space: 116915 Effective search space used: 116915 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: 49 (23.5 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