Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_005817430.1 DHAF_RS06735 glyoxylate reductase
Query= BRENDA::Q8RG11 (335 letters) >NCBI__GCF_000021925.1:WP_005817430.1 Length = 338 Score = 138 bits (347), Expect = 2e-37 Identities = 100/307 (32%), Positives = 149/307 (48%), Gaps = 21/307 (6%) Query: 33 LKVRLTEETANLTKGYDVVCGFANDNINKETIDIMAENGIKLLAMRCAGFNNVSLKDVNE 92 L++ EE KG D + +D I+K+ I+ A +K++A AG+NN+ + E Sbjct: 38 LRLLSKEEIIAGLKGKDALLCLLSDAIDKDIIE--ANPQLKVIANYGAGYNNIDIAAAGE 95 Query: 93 -RFKVVRVPAYSPHAIAEYTVGLILAVNRKINKAYVRTREGNFSINGLM---GIDLYEKT 148 V P S A A+ T GLILA+ R+I + TR G F + G+D+ KT Sbjct: 96 ANIPVTNTPDVSTDATADLTFGLILAIARRIVEGDKETRAGRFKGWAPLYHLGVDVTGKT 155 Query: 149 AGIIGTGKIGQILIKILRGFDMKVIAYDLFP-NQKVADELGFEYVSLDELYANSDIISLN 207 GIIG G IG+ + + +GFDMK++ +++ ELGF Y+SL+ + +D +SL+ Sbjct: 156 LGIIGMGNIGKAIARRAKGFDMKIVYTSRTRLSEQQEKELGFTYMSLEGVLKTADFVSLS 215 Query: 208 CPLTKDTKYMINRRSMLKMKDGVILVNTGRGMLIDSADLVEALKDKKIGAVALDVYEEEE 267 + T +MI R + MK L+NT RG L+D L++AL++K I ALDVYE Sbjct: 216 LSYSPATHHMIGERELETMKPSAYLINTARGPLVDEKALLKALENKSIAGAALDVYE--- 272 Query: 268 NYFFEDKSTQVIEDDILGRLLSFYNVLITSHQAYFTKEAVGAITVTTLNNIKDFVEGRPL 327 E I L V++T H T E A+ NI + G Sbjct: 273 -----------FEPQITAGLEKLDQVILTPHIGNATVETRDAMAEIAAGNIAAVLRGEAP 321 Query: 328 VNEVPQN 334 + V QN Sbjct: 322 LTCVNQN 328 Lambda K H 0.320 0.139 0.389 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: 256 Number of extensions: 16 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: 335 Length of database: 338 Length adjustment: 28 Effective length of query: 307 Effective length of database: 310 Effective search space: 95170 Effective search space used: 95170 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 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