Align D-lactate dehydrogenase; EC 1.1.1.28 (characterized)
to candidate WP_066330061.1 BLR17_RS12115 3-phosphoglycerate dehydrogenase
Query= CharProtDB::CH_091799 (329 letters) >NCBI__GCF_900100165.1:WP_066330061.1 Length = 316 Score = 119 bits (298), Expect = 1e-31 Identities = 90/276 (32%), Positives = 141/276 (51%), Gaps = 53/276 (19%) Query: 21 ESFGFELEFFDFLLTEKTAKTANGCEAVCIFVNDDGSRPVL----EELKKH------GVK 70 E GFE+ +T K A+ E V FVN++ VL +++K G+K Sbjct: 18 EKGGFEV------ITTKVAQ-----EQVANFVNENNVSVVLVRSATKVRKDIIDACPGLK 66 Query: 71 YIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRRIHRAYQRTRDA 130 I G +N+D+D AK G+ V+ PA E+VAE ++T R +H + + Sbjct: 67 IIGRGGVGMDNIDVDYAKSKGIHVINTPASSSESVAELVFAHLLTGVRFLHDS-----NR 121 Query: 131 NFSLEGLTGFT-----------MYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDPYPSA 179 N LEG T F + GKT G++G G+IG A ++ G GM+++A D + Sbjct: 122 NMPLEGDTKFNDLKKAYANGVELRGKTLGIVGIGRIGQATAKMALGLGMKVIAADSF--I 179 Query: 180 AALELGVEYVD------------LPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGV 227 +++ VE+ D L ++F+ESD I+LH P +N +++ E F MKNGV Sbjct: 180 PQVDVKVEFFDGQSITTTIKTQSLESVFAESDFITLHVPA--QNGYIVTEKEFATMKNGV 237 Query: 228 MIVNTSRGALIDSQAAIEALKNQKIGSLGMDVYENE 263 IVN +RG +I+ ++AL + K+ G+DV+ENE Sbjct: 238 GIVNCARGGVINEVDLVKALDSGKVAFAGLDVFENE 273 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: 234 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: 329 Length of database: 316 Length adjustment: 28 Effective length of query: 301 Effective length of database: 288 Effective search space: 86688 Effective search space used: 86688 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: 48 (23.1 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