Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CA265_RS10420 CA265_RS10420 hydroxyacid dehydrogenase
Query= BRENDA::A0A140N893 (329 letters) >FitnessBrowser__Pedo557:CA265_RS10420 Length = 334 Score = 340 bits (872), Expect = 3e-98 Identities = 165/323 (51%), Positives = 228/323 (70%), Gaps = 1/323 (0%) Query: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTAKTAN-GCEAVCIFVNDDGSRP 59 MK+ +S K YD ++ + N+ + FELEF++ L A G + VC+FVND + Sbjct: 1 MKIVFFSAKPYDHEFFESANKHYDFELEFWETHLGPHIADAIKAGTDVVCVFVNDKLTAE 60 Query: 60 VLEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRR 119 V+ L + GVK IALRCAGFNNVDL+AAK+ G++V RVPAY P+AVAEHA+ M++TLNR+ Sbjct: 61 VIATLAQKGVKIIALRCAGFNNVDLNAAKQHGIRVCRVPAYSPQAVAEHAVAMLLTLNRK 120 Query: 120 IHRAYQRTRDANFSLEGLTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSA 179 H+AY R R+ NFSL GL GF ++GKT GVIGTG+IG A +I+ GFG R++AFDP+ +A Sbjct: 121 THKAYNRVREQNFSLSGLMGFNLFGKTVGVIGTGEIGTAFCKIMLGFGCRVMAFDPFVNA 180 Query: 180 AALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFDQMKNGVMIVNTSRGALID 239 + GVEY+ + E+D+ISLHCPLTPEN++L+ + MK GV ++NTSRG LI+ Sbjct: 181 SLASAGVEYLPFHEVIKEADMISLHCPLTPENHYLIGSNSLSTMKKGVTLINTSRGGLIN 240 Query: 240 SQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTGHQAFL 299 ++ IEALK ++ +LG+DVYE E LFF+D S +I DD +RL + NVL TGHQAF Sbjct: 241 TREVIEALKTGQLAALGIDVYEQEEQLFFKDLSGSIIGDDDIQRLISFPNVLLTGHQAFF 300 Query: 300 TAEALTSISQTTLQNLSNLEKGE 322 T EALT I+++TL+ + L + + Sbjct: 301 TQEALTEIAESTLKTVKILSENK 323 Lambda K H 0.320 0.136 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: 277 Number of extensions: 3 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: 334 Length adjustment: 28 Effective length of query: 301 Effective length of database: 306 Effective search space: 92106 Effective search space used: 92106 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