Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate 6936424 Sama_0612 D-lactate dehydrogenase (RefSeq)
Query= CharProtDB::CH_091799 (329 letters) >FitnessBrowser__SB2B:6936424 Length = 329 Score = 417 bits (1071), Expect = e-121 Identities = 203/328 (61%), Positives = 252/328 (76%) Query: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPV 60 MK+ +S K YD ++ + N SFG +E+FD L +T K A G E +C FVND+ S V Sbjct: 1 MKIGFFSAKHYDMQHFDRTNASFGAHIEYFDSRLCMQTVKLAYGFEVICAFVNDELSAEV 60 Query: 61 LEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRI 120 L EL +G + IA+RCAGFNNVDL+ AK LG+ VV VPAY PE+VAEH + +M+TLNR+I Sbjct: 61 LNELHGNGTRVIAMRCAGFNNVDLEEAKHLGMTVVNVPAYSPESVAEHTVALMLTLNRKI 120 Query: 121 HRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSAA 180 H+AYQRTRDANFSLEGL GF M+GKT GVIGTGKIG+A +RIL GFG +++AFDP+PS A Sbjct: 121 HKAYQRTRDANFSLEGLVGFNMHGKTVGVIGTGKIGLATIRILLGFGCKVVAFDPFPSPA 180 Query: 181 ALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSRGALIDS 240 LGV Y++L L DV+SLHCPLT EN+HLL F +MK GVM++NTSRG L+++ Sbjct: 181 VEALGVPYLELDELLKLCDVVSLHCPLTKENHHLLRAETFAKMKPGVMVINTSRGGLLNA 240 Query: 241 QAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFLT 300 A+EALK +IG+LG+DVYENE++LFFEDKSN+VIQDDVFRRLSACHNV+FTGHQAFLT Sbjct: 241 FDAMEALKVGQIGALGLDVYENEKELFFEDKSNEVIQDDVFRRLSACHNVVFTGHQAFLT 300 Query: 301 AEALTSISQTTLQNLSNLEKGETCPNEL 328 EAL +I+ TTL N+ GE C NEL Sbjct: 301 EEALGAIATTTLTNVQKALAGERCGNEL 328 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: 338 Number of extensions: 10 Number of successful extensions: 1 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: 329 Length adjustment: 28 Effective length of query: 301 Effective length of database: 301 Effective search space: 90601 Effective search space used: 90601 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 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