Align L-lactate oxidase (EC 1.1.3.2) (characterized)
to candidate SM_b20850 SM_b20850 L-lactate dehydrogenase
Query= BRENDA::Q8Z0C8 (365 letters) >FitnessBrowser__Smeli:SM_b20850 Length = 378 Score = 257 bits (656), Expect = 4e-73 Identities = 150/371 (40%), Positives = 222/371 (59%), Gaps = 24/371 (6%) Query: 8 INLFEYEQLAKTHLSQMAFDYYISGAGDEITLQENRAVFERIKLRPRMLVDVSQINLTTS 67 + + + + LA+ + ++ FDY SGA E T + N F IKLR R+LVD+S +L T+ Sbjct: 5 LEIRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAGIKLRQRVLVDMSDRSLETT 64 Query: 68 VLGQPLQLPLLIAPMAFQCLAHTEGELATAMAAASAGTGMVLSTLSTKSLEEVAEVGSKF 127 ++GQ + +P+ +AP + H +GE+ A AA + G LST+S S+E+VA V +K Sbjct: 65 MIGQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTKP 124 Query: 128 SPSLQWFQLYIHKDRGLTRALVERAYAAGYKALCLTVDAPVLGQRERDRRNEFVLPPGL- 186 WFQLY+ ++R L++RA AA AL +T+D +LGQR +D RN PP L Sbjct: 125 F----WFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLT 180 Query: 187 --HLANLTT-------ISGLN-------IPHAPGESGLFTYFA---QQLNPALTWDDLEW 227 HL + T + G N + HA + L + A +Q +P L+W D+EW Sbjct: 181 PKHLWMMATRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEW 240 Query: 228 LQSLSPLPLVLKGILRGDDAARAVEYGAKAIVVSNHGGRQLDGAIASLDALPEIVAAVNG 287 ++ PL+LKGIL +DA A + GA AI+VSNHGGRQLDGA +S+ LP IV AV Sbjct: 241 IKERWGGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGD 300 Query: 288 KAEVLLDGGIRRGTDIIKALAIGAQAVLIGRPVLWGLAVGGQAGVSHVISLLQKELNVAM 347 + EV LDGGIR G D++KA+A+GA+ IGRP L+GL G+ GV+ + +++KE++ M Sbjct: 301 QIEVHLDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTM 360 Query: 348 ALIGCSQLQDI 358 AL G ++ ++ Sbjct: 361 ALCGKRRITEV 371 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: 300 Number of extensions: 9 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 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