Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate HSERO_RS01205 HSERO_RS01205 2-hydroxy-acid oxidase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__HerbieS:HSERO_RS01205 Length = 393 Score = 271 bits (693), Expect = 2e-77 Identities = 156/375 (41%), Positives = 218/375 (58%), Gaps = 28/375 (7%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 E +A+ + F+Y GA +EI+L+ NR VF RI PR LVDVS + GQ Sbjct: 19 ELRAMARKRVPNFCFEYVEGGAEEEISLRHNREVFTRIGFLPRTLVDVSVRRQGRRLFGQ 78 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 + P LI P F L EG++A A AAASAG VL+ +ST SLEEV + S + Sbjct: 79 DIASPFLIGPTGFSGLLAREGDVAMASAAASAGVPFVLTNVSTTSLEEVV----RRSGAQ 134 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 W Q+Y+++DR ++ +RA AAG L LT D+ V G+RE D RN F P L N Sbjct: 135 VWQQVYLYRDRAFVASVAQRAQAAGIGVLVLTTDSAVYGKREWDARN-FSSPRRLDWRNK 193 Query: 192 TTIS-------GLNIPHA------------PGESGL----FTYFAQQLNPALTWDDLEWL 228 + + PH P ++ + Q L+ AL W D++WL Sbjct: 194 LDVLRHPRWLIDILYPHGFPRFANLGDLLPPDQTSVRGAAAAILGQSLSAALDWADVQWL 253 Query: 229 QSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGK 288 + + P LVLKG+++ +DA RAV G IV+SNHGGRQLDGA++++D LPE+VAAV G+ Sbjct: 254 RGIWPGKLVLKGVMQVEDAQRAVALGVDGIVLSNHGGRQLDGALSTMDVLPEVVAAVKGQ 313 Query: 289 AEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMA 348 V+LDGG RRG DI+KA+A+GA AVL+GR +GLA GGQAG + + +L+ E++ +A Sbjct: 314 LTVMLDGGFRRGADIVKAIALGADAVLLGRATTYGLAAGGQAGATRALEILRSEVDRVLA 373 Query: 349 LIGCSQLQDIDTSFL 363 L+ C + +D S+L Sbjct: 374 LLACPDIDQLDASYL 388 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: 11 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: 393 Length adjustment: 30 Effective length of query: 335 Effective length of database: 363 Effective search space: 121605 Effective search space used: 121605 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