Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate AZOBR_RS27055 AZOBR_RS27055 L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__azobra:AZOBR_RS27055 Length = 384 Score = 213 bits (541), Expect = 9e-60 Identities = 137/380 (36%), Positives = 201/380 (52%), Gaps = 29/380 (7%) Query: 3 AISSPINLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQI 62 A+++ +N+ E Q A+ L + F+Y GA DE + ++ + + +PR+LVDVS+ Sbjct: 2 AVTASLNIAEARQRARARLPRGLFEYIDRGAEDETGIATSKTALDSLVFKPRVLVDVSKR 61 Query: 63 NLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVA- 121 + TT + G +PL++AP A L +GE+ A AAA+ G +ST S S+E +A Sbjct: 62 DATTRLFGVDQPMPLVVAPTAVAGLVWYDGEVELAKAAAAVGIPFCVSTQSITSVERIAG 121 Query: 122 EVGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFV 181 E G++ WFQLY+ + R TR LV RA AG +AL LTVD V RE + RN F Sbjct: 122 ESGARL-----WFQLYVWRSRERTRELVRRAERAGAEALVLTVDTAVTPNREYNVRNGFG 176 Query: 182 LP--PGLH-----LANLTTISGLNIPH-APGESGLFTYFAQQLNPAL------------- 220 +P P + LA+ +G+ + G + ++ + AL Sbjct: 177 IPIKPSVRAGLDCLAHPRWFAGVFAKYLRNGGVPTYAHYPDEFRTALGRVAVGDEIGLAQ 236 Query: 221 --TWDDLEWLQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDAL 278 W D+ L+ L+LKG+LR DDA +A E G IVVSNHG R LD AI + L Sbjct: 237 DVGWGDVRSLRDAWKGKLILKGVLRADDAEKAAELGVDGIVVSNHGARNLDHAIHPVRCL 296 Query: 279 PEIVAAVNGKAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISL 338 +I V + VL D G+RRG+ + L +GAQ VL+GR VL+GLA G AG V+ + Sbjct: 297 TDIAERVGDRVTVLADSGVRRGSHVAGYLGLGAQGVLLGRAVLYGLATDGAAGAQAVLEM 356 Query: 339 LQKELNVAMALIGCSQLQDI 358 +++EL M +G + DI Sbjct: 357 IRRELLTTMGFLGAPTVADI 376 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: 312 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 365 Length of database: 384 Length adjustment: 30 Effective length of query: 335 Effective length of database: 354 Effective search space: 118590 Effective search space used: 118590 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