Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate 17666 b3605 L-lactate dehydrogenase, FMN-linked (NCBI)
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Keio:17666 Length = 396 Score = 235 bits (599), Expect = 2e-66 Identities = 141/367 (38%), Positives = 200/367 (54%), Gaps = 24/367 (6%) Query: 12 EYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTSVLGQ 71 +Y A+ L F Y GA E TL+ N + LR R+L ++S ++L T++ + Sbjct: 8 DYRAAAQRILPPFLFHYMDGGAYSEYTLRRNVEDLSEVALRQRILKNMSDLSLETTLFNE 67 Query: 72 PLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKFSPSL 131 L +P+ +AP+ + GE+ A AA + G LST+S +EEVA + Sbjct: 68 KLSMPVALAPVGLCGMYARRGEVQAAKAADAHGIPFTLSTVSVCPIEEVAPAIKR----P 123 Query: 132 QWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGLHLANL 191 WFQLY+ +DRG R +ERA AAG L TVD P G R RD + P L Sbjct: 124 MWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPTPGARYRDAHSGMSGPNAAMRRYL 183 Query: 192 TTIS--------GLN-IPHAPGE--------SGLFTYFA---QQLNPALTWDDLEWLQSL 231 ++ GLN PH G +GL Y +P+++W DLEW++ Sbjct: 184 QAVTHPQWAWDVGLNGRPHDLGNISAYLGKPTGLEDYIGWLGNNFDPSISWKDLEWIRDF 243 Query: 232 SPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNGKAEV 291 P+V+KGIL +DA AV +GA IVVSNHGGRQLDG ++S ALP I AV G + Sbjct: 244 WDGPMVIKGILDPEDARDAVRFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGDIAI 303 Query: 292 LLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAMALIG 351 L D GIR G D+++ +A+GA VL+GR L+ LA GQAGV+++++L++KE+ VAM L G Sbjct: 304 LADSGIRNGLDVVRMIALGADTVLLGRAFLYALATAGQAGVANLLNLIEKEMKVAMTLTG 363 Query: 352 CSQLQDI 358 + +I Sbjct: 364 AKSISEI 370 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: 302 Number of extensions: 18 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: 1 Length of query: 365 Length of database: 396 Length adjustment: 30 Effective length of query: 335 Effective length of database: 366 Effective search space: 122610 Effective search space used: 122610 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