Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate BPHYT_RS31690 BPHYT_RS31690 hypothetical protein
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS31690 Length = 383 Score = 198 bits (504), Expect = 2e-55 Identities = 133/371 (35%), Positives = 186/371 (50%), Gaps = 24/371 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 ++ + A+ HL AF+ GAG++ + EN A F R R S + T +V G Sbjct: 3 DFVEPARKHLPAFAFNTLAGGAGNDAGVAENEAAFGRRFFVSRRFAPAST-DQTATVFGH 61 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 P +APM L + +L A AA + VLST ++ S+E + +V +P + Sbjct: 62 SYASPFGVAPMGLANLFYPGADLLLAQAAQAGNFPFVLSTAASTSIERITKV----APDV 117 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 W+QLY+ D L L+ R G L LTVD PV G+R R+ LP A L Sbjct: 118 SWYQLYLLSDDRLNAELLSRVAGCGVAVLVLTVDVPVAGRRNSAIRDGVTLPLRWTSALL 177 Query: 192 TTIS-------GL----------NIPHA--PGESGLFTYFAQQLNPALTWDDLEWLQSLS 232 + G+ PHA + A + L WDDL+ ++++ Sbjct: 178 ADVMRRPQWALGMLRHGAPKLENYAPHAGTADVGAASRHIASVMKMGLEWDDLKKVRAMW 237 Query: 233 PLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVL 292 P LV+KGIL DDAAR+V GA I VSNHGGRQL+GAIASLDAL EI AV V Sbjct: 238 PGKLVIKGILHPDDAARSVALGADGIWVSNHGGRQLEGAIASLDALSEIRRAVGRDTAVF 297 Query: 293 LDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGC 352 LDGG+R G DI+KA A+GA GR + +A G+ GV + +L++E+ V +A +G Sbjct: 298 LDGGVRTGEDILKACALGAGLCFSGRSFAFPVAAYGERGVRAAVEILKEEIRVGLAQLGV 357 Query: 353 SQLQDIDTSFL 363 L + + L Sbjct: 358 QSLSALTSDSL 368 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: 290 Number of extensions: 17 Number of successful extensions: 4 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: 383 Length adjustment: 30 Effective length of query: 335 Effective length of database: 353 Effective search space: 118255 Effective search space used: 118255 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