Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_117590923.1 BA79_RS05750 D-glycerate dehydrogenase
Query= BRENDA::O66939 (334 letters) >NCBI__GCF_000691145.1:WP_117590923.1 Length = 326 Score = 156 bits (395), Expect = 6e-43 Identities = 91/273 (33%), Positives = 149/273 (54%), Gaps = 20/273 (7%) Query: 53 KLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTL 112 K+ ++LL P+LK++ SVG+D+ DL+ +++G++ TH P +VA+ F++IL+ Sbjct: 56 KIDQDLLDHAPQLKVVSNNSVGYDNFDLEAMRQRGVIGTHTPYTLDHTVADLAFSLILSS 115 Query: 113 VKRLKRIEDRVKK---LNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGL-AFGMKVL 168 +R+ ++ ++K F Q+ +I +++ TLG+IG GRIG +VA F M VL Sbjct: 116 ARRIAELDRFIRKGKWTKFVQEEDIFGIDVHHQTLGIIGMGRIGEQVAKRAAHGFDMNVL 175 Query: 169 CYDVVKREDLKEK-GCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLI 227 ++ + E + G VY +LD+LLK++D+I L P T ET+HMI E + LMK + Sbjct: 176 YHNRSRNEKAESAYGAVYCALDDLLKQADIIVLITPLTDETYHMIGERELKLMKPTALFV 235 Query: 228 NTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKD 287 N +RGK VD +L +A Q G G GLDV+E E + + E D Sbjct: 236 NISRGKTVDEKSLIQALQEGWIKGAGLDVYEQEPLQEDHPFKE---------------MD 280 Query: 288 NVIITPHIAYYTDKSLERIREETVKVVKAFVKG 320 NV + PHI T+ + + + + + V + G Sbjct: 281 NVTLAPHIGSATETTRDLMLKRAIHNVLHGIDG 313 Lambda K H 0.319 0.138 0.383 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: 295 Number of extensions: 19 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: 334 Length of database: 326 Length adjustment: 28 Effective length of query: 306 Effective length of database: 298 Effective search space: 91188 Effective search space used: 91188 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 (21.7 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