Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_019867321.1 METMI_RS0116070 D-glycerate dehydrogenase
Query= BRENDA::O66939 (334 letters) >NCBI__GCF_000384075.1:WP_019867321.1 Length = 323 Score = 124 bits (312), Expect = 2e-33 Identities = 92/292 (31%), Positives = 155/292 (53%), Gaps = 31/292 (10%) Query: 40 LKKAELISVFVYDKLTEELLS-KMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSP 98 ++ A+ + V D +T +++ + R+K+I VG+++ID++ K G++VT+ P Sbjct: 44 MQTADALLPTVTDPITSDIIGVENRRVKVIGNFGVGYNNIDINSAKGHGMVVTNTPHVLT 103 Query: 99 ESVAEHTFAMILTLVKRLKRIEDRV--KKLNFSQDSEILARELNRLTLGVIGTGRIG--- 153 + A+ ++L +R E + K+ ++++ +++ TLG+IG GRI Sbjct: 104 DCTADIAMLLLLMSARRAAEGERLILNKQWKGWGPTQLVGQKVTGKTLGLIGFGRIAQAM 163 Query: 154 SRVAMYGLAFGMKVLCY-----DVVKREDLKEKGCVYTSLDELLKESDVISLHVPYTKET 208 +R A +G FGMK+L Y D E+L+ C SL+ELL E+ +SLH P T Sbjct: 164 ARKAHHG--FGMKILFYVPSAPDPAIVEELQAVRC--GSLEELLTEAHFVSLHCPGGAAT 219 Query: 209 HHMINEERISLMKDGVYLINTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKY 268 H++N +R+ LM+ +LINTARG VVD+DAL +A + +G GLDV+E+E L Sbjct: 220 KHLLNGQRLKLMRPSAHLINTARGDVVDSDALIKALKERWIAGAGLDVYENEPHL----- 274 Query: 269 TEGKATDKNLKILELACKDNVIITPHIAYYTDKSLERIREETVKVVKAFVKG 320 N LEL DNV + PH+ ++++ + + + AF G Sbjct: 275 --------NPGFLEL---DNVTLLPHLGSASEETRVAMGNRVLANIAAFFAG 315 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: 254 Number of extensions: 11 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: 323 Length adjustment: 28 Effective length of query: 306 Effective length of database: 295 Effective search space: 90270 Effective search space used: 90270 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