Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate GFF927 PGA1_c09430 l-lactate dehydrogenase IldD
Query= BRENDA::F8WQN2 (384 letters) >FitnessBrowser__Phaeo:GFF927 Length = 401 Score = 186 bits (473), Expect = 8e-52 Identities = 119/386 (30%), Positives = 190/386 (49%), Gaps = 33/386 (8%) Query: 9 LEEVEEEAKKVMPKMAFDYYSTGSDTCYTVGENRSCFSRYLLLPRMLRNVSRVDTSHELF 68 L ++ + A++ +P+ ++Y +G+ T T NR+ + P +L D S Sbjct: 13 LSDLRQRARRRLPRFVWEYLDSGTGTEATKARNRAALDQLGFAPSILHGPQTPDLSRRFL 72 Query: 69 GIRSSMPVWVAPMAMHGLAHPGREVATCRAAAAAGVPFTFSTVATSSLQEIQETGHDNRI 128 GI +P VAP+ M GL P E R AAA G+P+ STVA+ S +++ + Sbjct: 73 GIDRPLPFGVAPVGMSGLIWPDAERLLARCAAAQGLPYCLSTVASQSPEDLVDDLGAAPW 132 Query: 129 FQLYVIRNREVVRRWVTEAESRGFKALMVTVDAQRLGNREADARNKFTLPP--------- 179 FQLY ++ ++ R + A++ GF L++TVD RE R+ T PP Sbjct: 133 FQLYPPKDPDIRRDLLARAKAAGFAGLVLTVDVPVASRRERQTRSGLTQPPRLTPRLLAQ 192 Query: 180 ---------GLALRNLEYLSSASTVQARDSQDGSGLMKLFTSEVD----DSLTWEFIPWL 226 G+A R L ++ + T + G+G T+ V S W+++ WL Sbjct: 193 VAMRPAWAVGMARRGLPHMKTLDTYVS-----GAGASLSSTAHVGYLLRTSPDWDYVQWL 247 Query: 227 RGVTKLPIIVKGLLSPADAELAVQYGVDGIVVSNHGGRQLDYAPSGLHMLPAVVAAVRGC 286 R P+I+KG++ DA G D + VSNH GRQ D APS + LP + AA R Sbjct: 248 RDHWDGPLIIKGVMRAEDAAPLEAIGADALWVSNHAGRQFDAAPSTIEALPGIRAATR-- 305 Query: 287 GSSIPVLVDGGVRRGTDVIKALALGASGVLLGRPVLYGLAVGGQAGVERVLQLLRSEIEL 346 +P++ D G+ G D+++ALALGA V+LGR + LA G G + ++ +LR +++ Sbjct: 306 ---LPLIFDSGIESGLDILRALALGADYVMLGRAFHFALAALGSRGPDHLVDILRKDLDA 362 Query: 347 SMALAGCSSVQQIGPQLLLPAPSAGP 372 +M G ++ + P+ L A A P Sbjct: 363 NMGQLGLETLSAL-PRPLGLASFANP 387 Lambda K H 0.320 0.135 0.396 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: 299 Number of extensions: 16 Number of successful extensions: 6 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: 384 Length of database: 401 Length adjustment: 31 Effective length of query: 353 Effective length of database: 370 Effective search space: 130610 Effective search space used: 130610 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