Align D-lactate dehydrogenase; D-LDH; EC 1.1.1.28; D-specific 2-hydroxyacid dehydrogenase (uncharacterized)
to candidate WP_057687229.1 ABB28_RS15235 D-glycerate dehydrogenase
Query= curated2:O83080 (331 letters) >NCBI__GCF_001431535.1:WP_057687229.1 Length = 345 Score = 114 bits (285), Expect = 4e-30 Identities = 84/263 (31%), Positives = 126/263 (47%), Gaps = 22/263 (8%) Query: 41 ELLKGYEGLVVMQFLAMEDEVYDYMGACKLKVLSTRTAGFDMYNATLLKKHGIRLTNVPS 100 E L+G +G ++ L GA +L+V++ G++ + L G+ +N P Sbjct: 44 ERLRGVDGAIIT--LNERIGAAQLAGADRLQVIANVGVGYNNLDVDALSAAGVLASNTPD 101 Query: 101 YSPNAIGEYALAAALQLTRHAREIETFVRKRDF-RWQ-KPILSKELRCSRVGILGTGRIG 158 + A + R E E ++R + +W + +L ++ S +GILG GRIG Sbjct: 102 VLTETTADLGFALLMAAARRITESERWLRDGQWGQWSFQTMLGADIHGSTLGILGMGRIG 161 Query: 159 QAAARL-FKGVGAQVVGFDPYPNDAAKE---WLTYVSMDELLSTSDVISLHMPATKDSHH 214 Q AR G G +V+ + AA E Y +D LL+ SD + L +P T SHH Sbjct: 162 QGIARRGAHGFGMRVLYHNRSRLPAATEAEVGAQYAELDALLAQSDHLVLVLPYTAASHH 221 Query: 215 LINAKTIAQMKDGVYLVNTARGAVIDSQALLDSLDKGKIAGAALDAYEFEGPYIPKDNGN 274 LINA +A+MK LVN ARG ++D AL D+L G++A A LD YE E P+ Sbjct: 222 LINASALAKMKPTATLVNIARGGIVDELALADALAHGRLAAAGLDVYEGEPQVRPE---- 277 Query: 275 NPITDTVYARLVAHERIIYTPHI 297 L+A ++ TPHI Sbjct: 278 ----------LLALRNVVLTPHI 290 Lambda K H 0.319 0.135 0.396 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: 245 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: 331 Length of database: 345 Length adjustment: 28 Effective length of query: 303 Effective length of database: 317 Effective search space: 96051 Effective search space used: 96051 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 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