Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_084235747.1 HTA01S_RS00900 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_001592305.1:WP_084235747.1 Length = 417 Score = 318 bits (814), Expect = 2e-91 Identities = 178/353 (50%), Positives = 235/353 (66%), Gaps = 11/353 (3%) Query: 8 INLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTS 67 +NL ++E A+T LS A Y+ GA D TL++N ++RI L PR+L ++ + Sbjct: 47 VNLADHEAFARTVLSPQADAYFNGGAADGFTLRDNALAWQRIALLPRVLQPLAGGHTRVE 106 Query: 68 VLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAE-VGSK 126 +LG+ L P+L+AP+A+Q LAH GE+ATA+AAA G G+VLST ++ LE+VA V ++ Sbjct: 107 LLGRTLAHPILVAPIAYQRLAHPHGEVATALAAAVLGAGLVLSTQASTPLEDVARLVLAE 166 Query: 127 FSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGL 186 + WFQLY+ DRG TR LV RA AAGY+AL LTVDAPV G R+R+RR F LPPG+ Sbjct: 167 NARGPLWFQLYLQVDRGFTRELVHRAEAAGYEALVLTVDAPVNGARDRERRAGFTLPPGI 226 Query: 187 HLANLTTISGLNIPHA----PGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVLKGIL 242 NL GL P PG+S LF L A TWDD+ WL+S++ LP++LKGI Sbjct: 227 SAVNL---QGLRKPAPAALQPGQSALFD---DLLTHAPTWDDVAWLRSITRLPVLLKGIT 280 Query: 243 RGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRGTD 302 DA AV+ GA ++VSNHGGR LD A+ LP + AV G VL+DGGIRRGTD Sbjct: 281 HPADARLAVDAGAAGLIVSNHGGRTLDTMPATATLLPAVAQAVGGAVPVLVDGGIRRGTD 340 Query: 303 IIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQL 355 ++KA+A+GA AVL+GRPV+ GLA G GV+HVI LL+ EL +AMAL GC++L Sbjct: 341 VLKAIALGASAVLVGRPVVHGLANAGATGVAHVIRLLRDELEIAMALCGCARL 393 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: 406 Number of extensions: 24 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: 417 Length adjustment: 31 Effective length of query: 334 Effective length of database: 386 Effective search space: 128924 Effective search space used: 128924 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