Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate Echvi_3936 Echvi_3936 Lactate dehydrogenase and related dehydrogenases
Query= CharProtDB::CH_091799 (329 letters) >FitnessBrowser__Cola:Echvi_3936 Length = 330 Score = 348 bits (893), Expect = e-100 Identities = 177/329 (53%), Positives = 231/329 (70%), Gaps = 3/329 (0%) Query: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60 MK+ +S +++ YL++ EL+ + LT T A G +AV IFV D+GSRPV Sbjct: 1 MKITAFSAHKFEHSYLKEALSDH--ELKLLEVRLTMDTVDLAAGSDAVAIFVTDNGSRPV 58 Query: 61 LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120 LE+L++ GVKY+ALR AGFN+VDL AA+ELGLKV RVP Y P A+AEH + +M+ LNR++ Sbjct: 59 LEKLQQFGVKYLALRSAGFNHVDLSAAEELGLKVARVPEYSPAAIAEHTVALMLALNRKL 118 Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPY-PSA 179 +A+ R RD NFSL+GL GF M GKT G+ GTGKIG + + L GFG RLLA+DPY + Sbjct: 119 VKAHNRVRDLNFSLDGLVGFDMEGKTIGIAGTGKIGSKVAKTLSGFGCRLLAYDPYINES 178 Query: 180 AALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSRGALID 239 EL +EYVD TL +ESD+I+LH PL+ + +++N ++ E MK GVM++NTSRGAL++ Sbjct: 179 LKAELEIEYVDFKTLCTESDIITLHLPLSSSSQYMINSSSMEDMKKGVMLINTSRGALVN 238 Query: 240 SQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFL 299 ++ IEALK KIGS GMDVYE E DLFFED S D++QDDV RL NVL T HQAFL Sbjct: 239 TKEVIEALKTGKIGSFGMDVYEEEEDLFFEDHSEDILQDDVIARLLTFQNVLITSHQAFL 298 Query: 300 TAEALTSISQTTLQNLSNLEKGETCPNEL 328 T EAL I+ T NL+ K E+ P+EL Sbjct: 299 TKEALEKIAGVTAFNLNCWAKNESSPHEL 327 Lambda K H 0.320 0.136 0.388 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: 276 Number of extensions: 9 Number of successful extensions: 2 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: 329 Length of database: 330 Length adjustment: 28 Effective length of query: 301 Effective length of database: 302 Effective search space: 90902 Effective search space used: 90902 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 17 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