Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate WP_061533167.1 CAter10_RS09135 alpha-hydroxy-acid oxidizing protein
Query= BRENDA::Q8Z0C8 (365 letters) >NCBI__GCF_001584165.1:WP_061533167.1 Length = 378 Score = 259 bits (663), Expect = 6e-74 Identities = 149/367 (40%), Positives = 217/367 (59%), Gaps = 23/367 (6%) Query: 16 LAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQPLQL 75 LA+ + + +DY SG+ E T + N +KLR R+ ++V Q + ++++GQ + + Sbjct: 13 LAQKRVPKAFYDYADSGSYTESTYRANSDDLAALKLRQRVAINVDQRSTRSTMIGQDVTM 72 Query: 76 PLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSLQWFQ 135 P+ IAP + GE+ A+AA G LST+S S+E+VA V +K WFQ Sbjct: 73 PVAIAPTGLTGMQWANGEMLGAIAAEKFGIPFTLSTMSICSIEDVASVTTKPF----WFQ 128 Query: 136 LYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANLTTIS 195 LY+ +DRG ++L+ERA AA AL LT+D +LGQR +D +N +PP + LANL ++ Sbjct: 129 LYVMRDRGFIKSLIERAKAAKCSALVLTLDLQILGQRHKDLKNGMSVPPKMTLANLIDLA 188 Query: 196 ----------------GLNIPHAPGESGLFT---YFAQQLNPALTWDDLEWLQSLSPLPL 236 G H G G+ T + A Q +P L WDD+ W++ L Sbjct: 189 SKPGWALRALGGRKSFGNLAGHVKGADGIMTLSKWTASQFDPTLCWDDIAWIKEQWGGKL 248 Query: 237 VLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEVLLDGG 296 +LKGIL +DA A GA AIVVSNHGGRQLDGA++S+ ALP IV AV + EV DGG Sbjct: 249 ILKGILDVEDAKIAATTGADAIVVSNHGGRQLDGAVSSISALPAIVDAVGDQIEVWFDGG 308 Query: 297 IRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIGCSQLQ 356 IR G D++KA+A+GA+ +IGR L+ L G+AGV+ ++ +LQ+EL+V+MAL G ++ Sbjct: 309 IRSGQDVLKAVALGAKGTMIGRAFLYSLGAMGEAGVTRMLQILQQELDVSMALTGNKDIK 368 Query: 357 DIDTSFL 363 D+ L Sbjct: 369 DVGPHIL 375 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: 307 Number of extensions: 11 Number of successful extensions: 4 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: 378 Length adjustment: 30 Effective length of query: 335 Effective length of database: 348 Effective search space: 116580 Effective search space used: 116580 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 24 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