Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate GFF755 PGA1_c07690 (S)-mandelate dehydrogenase MdlB
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Phaeo:GFF755 Length = 363 Score = 192 bits (487), Expect = 2e-53 Identities = 132/351 (37%), Positives = 180/351 (51%), Gaps = 21/351 (5%) Query: 15 QLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQ 74 +LA+ L M FDY AG E NRA + I LRPR+L DVSQ +L TS+ G Sbjct: 14 RLARRRLPWMVFDYIDGAAGQETGAARNRAALDAITLRPRILRDVSQRSLATSIFGAETD 73 Query: 75 LPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSLQWF 134 P IAPM LA +L A AA +ST+++ LE + E ++ WF Sbjct: 74 RPFGIAPMGMCNLAAPGADLMLARLAAHHRVPHGVSTVASTPLEILLEAAEGYA----WF 129 Query: 135 QLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLP----------- 183 QLY D T L ERA AAGY+ L LTVD P +G+R R+ R+ F +P Sbjct: 130 QLYFSGDGTGTFKLAERARAAGYQTLVLTVDVPEVGRRPRELRHGFKMPFRIGPRQFIDF 189 Query: 184 ---PGLHLANLTTISGLNIPHAPGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVLKG 240 P LA L + G + A E + + + TWD L L+ L P LV+KG Sbjct: 190 ALHPRWSLATL--LKGKPVM-ANFEMEGYDFDRTESRARATWDTLARLRDLWPGKLVVKG 246 Query: 241 ILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIRRG 300 +L +DA V GA AI +S+HG RQL+ A A ++ L +I A V D GIR G Sbjct: 247 VLDVEDARALVSAGADAIQISSHGARQLEAAPAPIEMLAKIRADFGPTFPVFYDSGIRSG 306 Query: 301 TDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 D++KA+ GA V +GR + + +A G+AG+ + L +EL++AMA G Sbjct: 307 EDVLKAITTGADFVFLGRILQYAIAARGEAGLEQLWDALSEELSIAMAQTG 357 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: 267 Number of extensions: 10 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: 363 Length adjustment: 29 Effective length of query: 336 Effective length of database: 334 Effective search space: 112224 Effective search space used: 112224 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 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