Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate Dsui_1668 Dsui_1668 alpha-hydroxyacid dehydrogenase, FMN-dependent L-lactate dehydrogenase
Query= BRENDA::W1QKE8 (558 letters) >FitnessBrowser__PS:Dsui_1668 Length = 374 Score = 224 bits (570), Expect = 6e-63 Identities = 130/360 (36%), Positives = 196/360 (54%), Gaps = 20/360 (5%) Query: 173 EVMNLHDFEYIAKKILPKGAWAYYSSGADDEVSMRENHYAYQRIYFRPRVLVDVSKVDTS 232 E+ + D+E A++ L AW Y SG+ DE++ R N A+ R+ RVL DV T Sbjct: 14 EIAAVGDYEPYARRRLDDNAWTYLHSGSADELTFRWNKEAFDRLRLNGRVLADVRGGHTR 73 Query: 233 TTLLGTPTSVPFYVSATALAKLGHPDGECSIARGAGKEGVIQMISTLASNSLEEIAAARV 292 L G P +++ A KL HP+GE + GAG ++STLAS LE+IAA Sbjct: 74 LELFGQRYEHPLFLAPVAHQKLFHPEGELATVLGAGALQAGMVVSTLASTPLEDIAAQ-- 131 Query: 293 PGATQWFQLYVNEDRNVAFEMVKKAEKLGIKAIFVTVDAPSLGNREKDARVKFEGESDVQ 352 A WFQLY DR+ ++V++AE G +A+ VTVD P G R ++ R+ F + + Sbjct: 132 AEAPLWFQLYFQPDRDFTRQLVQRAEAAGYQALVVTVDVPIFGLRNREQRIGFHLPAGID 191 Query: 353 KSN--------EVVRSQGASRALSSFIDTRLTWDDVKKIKQSTKLPVLIKGVQRLEDVVQ 404 +N + G S + TW+D+ ++ T+LP+++KG+ D Q Sbjct: 192 PANLRGMAAPAQPALHPGQSIVFDGIMAAAPTWEDIAWVRSLTRLPLILKGITHPGDARQ 251 Query: 405 AVDDGFDGVVLSNHGGRQLDTAPPPVELLAEVVPELKRRNKLRPDFEIFIDGGVRRGTDI 464 A D G DG+++SNHGGR LDT P +E L VV + R + +DGG+RRG+D+ Sbjct: 252 AADLGVDGLIVSNHGGRSLDTLPASIEALPAVVQAVAGR------LPVLLDGGIRRGSDV 305 Query: 465 LKALALGGQNVRVGVGLGRPFLYANSSYGENGVRKAIQLLKDELEMDMRLLGVRNLRELD 524 +KALALG V LGRP++Y ++ G GV ++LL++ELE+ M + G L +++ Sbjct: 306 VKALALGA----AAVLLGRPWVYGLAAAGPLGVAHTLKLLREELEVTMAMAGCTTLADIN 361 Lambda K H 0.317 0.135 0.393 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: 480 Number of extensions: 22 Number of successful extensions: 5 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: 558 Length of database: 374 Length adjustment: 33 Effective length of query: 525 Effective length of database: 341 Effective search space: 179025 Effective search space used: 179025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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