Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_011604720.1 FRAAL_RS15640 alpha-hydroxy-acid oxidizing enzyme
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_000058485.1:WP_011604720.1 Length = 392 Score = 214 bits (546), Expect = 2e-60 Identities = 141/372 (37%), Positives = 210/372 (56%), Gaps = 34/372 (9%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 E ++ A+ L + + ++G +T+ +N F +K+RPR+ + +L+T+V+GQ Sbjct: 13 EAQRRARKRLPRGVYQALVAGTEAGVTMNDNVDAFGELKIRPRVADLPATRDLSTTVMGQ 72 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + P+LI+P Q + H +GE+A A AAA AGT M LS+ ++K +EEV V K Sbjct: 73 QISFPVLISPTGVQAV-HPDGEVAVARAAAGAGTAMGLSSFASKPVEEVGAVNDKLL--- 128 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFV---------- 181 FQ Y R A ERA +AG K L +T+D + RD + F+ Sbjct: 129 --FQTYWVGSREEILARAERARSAGAKGLIVTLDW--VFDSRRDWGSPFIPEKLDLRAMA 184 Query: 182 -------LPPGLHLANLT---TISGLNIPH-APGESGLFTYFAQQLN----PALTWDDLE 226 L PG +LA ++ L +P+ P E+ T+F P TW DL Sbjct: 185 RYAPQVALRPG-YLARWLRSRSLPDLGVPNLGPREATPPTFFGAYGQWIGTPPPTWSDLA 243 Query: 227 WLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVN 286 WL+ P ++KGI R DDA RAV+ GA AI VSNHGG LD AS+ LP +V AV Sbjct: 244 WLREQWGGPFMIKGITRPDDARRAVDVGASAISVSNHGGNNLDSTPASIRCLPGVVDAVG 303 Query: 287 GKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVA 346 + EVLLDGGIRRG+D++KALA+GA+AVLIGR L+G+A GG+ GV++V+ +L++ ++ Sbjct: 304 DQVEVLLDGGIRRGSDVVKALALGARAVLIGRAALFGMAAGGERGVTNVLEILRQGVSET 363 Query: 347 MALIGCSQLQDI 358 + +G + L ++ Sbjct: 364 LLGLGHASLHEL 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: 320 Number of extensions: 17 Number of successful extensions: 5 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: 392 Length adjustment: 30 Effective length of query: 335 Effective length of database: 362 Effective search space: 121270 Effective search space used: 121270 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