Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (uncharacterized)
to candidate WP_067078821.1 MCUHO_RS09440 malate dehydrogenase
Query= curated2:B8DSV5 (320 letters) >NCBI__GCF_001602375.1:WP_067078821.1 Length = 317 Score = 171 bits (434), Expect = 2e-47 Identities = 96/246 (39%), Positives = 145/246 (58%), Gaps = 14/246 (5%) Query: 75 RDADMVVITAGARQKPGQSRLDLAGATINIMKSIIPNMLKVAPNAIYMLITNPVDIVTHV 134 +D+D+++ TAG ++PGQ R DLA I+ + + +P+AI L+TNPVD++T V Sbjct: 72 KDSDVIICTAGVPRRPGQDRNDLAFENAKIIAETAETIGRTSPDAILFLVTNPVDVMTAV 131 Query: 135 AMKLSGLPASRMFGSGTNLDSARLRFLIAQQTGVNVKNVHAYIAGEHGDSEVPLWASATI 194 A+K SG ++FG GT+LDS RL+ LIA V+V VH I GEHGDS VPLW++ TI Sbjct: 132 ALKYSGFQPRQIFGLGTHLDSMRLKSLIAHYFRVHVSEVHTRIIGEHGDSMVPLWSATTI 191 Query: 195 GGVPMCD---WQALPGHEPLDAEARERIHQEVKNAAYKIINGKGATNYAISMSGVDIIEA 251 GG+ + + + LP E ++ V+ + II KG+T Y + ++ Sbjct: 192 GGIRITNLPTFSGLPTQEMIET---------VRTSGEAIIRDKGSTVYGPGEAIATLVRT 242 Query: 252 ILKDSNRILPVSSLL-SDFHGISDVCMSVPTLLNRNGVNSRINTPVSDRELAALKRSAET 310 IL D NR+L VSS + S+ HGI DVC+ VP +NR+GV + + + E+A + S + Sbjct: 243 ILGDENRVLTVSSYIKSEIHGIGDVCIGVPARINRDGV-FPVPLSLEEDEVAGFRESVKK 301 Query: 311 LRETAA 316 +R+ A Sbjct: 302 IRKVTA 307 Lambda K H 0.317 0.132 0.375 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: 249 Number of extensions: 6 Number of successful extensions: 3 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: 320 Length of database: 317 Length adjustment: 27 Effective length of query: 293 Effective length of database: 290 Effective search space: 84970 Effective search space used: 84970 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 (21.7 bits) S2: 48 (23.1 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