Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate 3609095 Dshi_2484 FMN-dependent alpha-hydroxy acid dehydrogenase (RefSeq)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Dino:3609095 Length = 389 Score = 167 bits (422), Expect = 6e-46 Identities = 121/366 (33%), Positives = 180/366 (49%), Gaps = 24/366 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGD-EITLQENRAVFERIKLRPRMLVDVSQINLTTSVLG 70 + + A+ + F+Y S GD EI +Q RA + I L P +L L T +LG Sbjct: 12 DLRRAARRRIPGFVFEYLDSATGDREIGVQTTRAALDAIHLLPGILHGQITPELETPLLG 71 Query: 71 QPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPS 130 Q P IAP+ L + E A AA+A LST++T++ E V V + Sbjct: 72 QTYARPFGIAPVGMSGLIWPDAERLLAAEAATARIPYGLSTVATQTPERVGPVAGEMG-- 129 Query: 131 LQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLH--- 187 WFQLY D G+ ++ RA A+G+ L LTVD P +RER RR +PP + Sbjct: 130 --WFQLYPPADPGIRDDIMARARASGFGTLVLTVDVPADSRRERQRRANLTIPPKITPRM 187 Query: 188 ----LANLTTISGLNIPHAPG---------ESGLFTYFA---QQLNPALTWDDLEWLQSL 231 + + T G+ P ++G +Y A + + A W L+ +++ Sbjct: 188 IFQMILHPTWALGMARHGTPSLKLAESYVEKTGAASYMAHAGKAIRGAPDWAYLDAVRAG 247 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 PLV+KG+LR +DA R G AI VS+H RQ +G ++ LP I AV V Sbjct: 248 WDGPLVVKGVLRPEDAVRLRAAGVDAIWVSDHSARQFEGGPGAITQLPAIRRAVGPDCPV 307 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 + D GI G DI++A+ +GA V++GR + LA G AGV H+I +L ++L M + G Sbjct: 308 IYDSGIEGGLDILRAVGLGADFVMLGRAWHFALAGLGPAGVRHLIHILTQDLVTNMQICG 367 Query: 352 CSQLQD 357 ++L D Sbjct: 368 IAKLAD 373 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: 16 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: 389 Length adjustment: 30 Effective length of query: 335 Effective length of database: 359 Effective search space: 120265 Effective search space used: 120265 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