Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate AZOBR_RS19085 AZOBR_RS19085 glycolate oxidase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__azobra:AZOBR_RS19085 Length = 362 Score = 288 bits (737), Expect = 2e-82 Identities = 171/365 (46%), Positives = 226/365 (61%), Gaps = 11/365 (3%) Query: 1 MTAISSPINLFEYEQLAKTHLSQMAFDYYISGAG-DEITLQENRAVFERIKLRPRMLVDV 59 M+ + ++L++YE+ + A YI+G G D IT Q NR ++R++L PR L D+ Sbjct: 1 MSVPADTVSLYDYERHFTARVDA-ATRAYIAGTGADGITRQANRDAYDRMRLMPRALRDL 59 Query: 60 SQINLTTSVLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEE 119 S + TS+ GQ + P+LIAPMAF L H +GE ATA AA GT M +ST S+ +LEE Sbjct: 60 SGASAATSLFGQAMPYPILIAPMAFHRLVHRDGERATAQAAGLTGTWMTVSTQSSVTLEE 119 Query: 120 VAEVGSKFSPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNE 179 VA WFQ+Y T ALV RA AAGY+AL LTVDAPV G R ++R Sbjct: 120 VAAAAG----GPLWFQIYTQPRPEDTLALVRRAEAAGYRALVLTVDAPVSGLRNIEQRAG 175 Query: 180 FVLPPGLHLANLTTISGLNI-PHAPGESGLFTYFAQQLNPALTWDDLEWLQSLSPLPLVL 238 F LP G+ NL ++ + P PG F L+ A +WD + WL + + LP++L Sbjct: 176 FRLPDGIAPVNLAGLAPDSFTPTRPGSP----VFQGMLHAAASWDTVRWLCAETRLPVLL 231 Query: 239 KGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGGIR 298 KGI+ DD AVE GA I+VSNHGGR LD A + LP + G+ +L DGGIR Sbjct: 232 KGIMNPDDVDLAVEAGAAGIIVSNHGGRTLDTLPAVAEVLPLVATRAAGRLPILADGGIR 291 Query: 299 RGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQDI 358 RGTDI+KALA+GA AVL+G+PVL LAVGG AGV+H++++LQ EL VAMAL G ++L DI Sbjct: 292 RGTDILKALALGADAVLVGQPVLHALAVGGMAGVAHMLTILQTELEVAMALSGRARLADI 351 Query: 359 DTSFL 363 D S + Sbjct: 352 DRSVI 356 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: 335 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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