Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_084057910.1 B9A12_RS10820 D-glycerate dehydrogenase
Query= BRENDA::O66939 (334 letters) >NCBI__GCF_900176285.1:WP_084057910.1 Length = 330 Score = 166 bits (421), Expect = 6e-46 Identities = 112/327 (34%), Positives = 175/327 (53%), Gaps = 24/327 (7%) Query: 1 MNVLFTS-VPQEDVPFYQEALKDLSLKIYTTDVSKVPE-NELKKAELISVFVYDKLTEEL 58 M VL T+ +P+ V +EA ++ + ++ + + N ++ + + D++ E+ Sbjct: 1 MKVLVTARLPEAVVGKIREAGHEVDMHLHMAPLERDQLLNRMEGVAGLLSTITDRIDGEV 60 Query: 59 LSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTLVKRLKR 118 + P L+++ VGFDHID+ ++GILVT+ P ++ A+ TFA+IL + +R+ Sbjct: 61 FDRAPGLRVVANYGVGFDHIDVAEATRRGILVTNTPGVLTDATADLTFALILAVARRVVE 120 Query: 119 IEDRVK--KLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGLAFGMKVLCYDVVK-- 174 + R + K F L E++ TLG++G GRIG VA F M+VL Y K Sbjct: 121 GDHRTRSGKFQFWAPLHFLGTEVSGKTLGIVGLGRIGRAVARRARGFDMQVL-YTARKPL 179 Query: 175 -REDLKEKGCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLINTARGK 233 R++ + G + LD+LL SD +SLHVP T ETHH+I +SLMK YLINTARG Sbjct: 180 GRDEEERLGVRFAPLDQLLARSDFVSLHVPLTPETHHLIGARELSLMKPFAYLINTARGP 239 Query: 234 VVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITP 293 VVD AL A ++ + G GLDV+E+E L T G LA NV++ P Sbjct: 240 VVDETALLEALRQRRIGGAGLDVYENEPQL-----TPG-----------LADLQNVVLLP 283 Query: 294 HIAYYTDKSLERIREETVKVVKAFVKG 320 H+ T ++ R+ + V+ + A + G Sbjct: 284 HVGSATVETRTRMAQMAVENLLAGLSG 310 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: 250 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: 334 Length of database: 330 Length adjustment: 28 Effective length of query: 306 Effective length of database: 302 Effective search space: 92412 Effective search space used: 92412 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 Apr 09 2024. 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