Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_011021352.1 MA_RS06920 NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9I530 (329 letters) >NCBI__GCF_000007345.1:WP_011021352.1 Length = 319 Score = 182 bits (462), Expect = 1e-50 Identities = 109/259 (42%), Positives = 156/259 (60%), Gaps = 14/259 (5%) Query: 70 RLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTRE 129 ++++L G+++VDL A G+ V +VP+Y+ +VAE L L L RR+H A RE Sbjct: 67 KMISLWQTGFDNVDLEEATDHGVIVSNVPSYAFESVAEFVFALTLNLLRRVHLADMNLRE 126 Query: 130 GDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNP-RIQALGGRY 188 G F G L K +GV+GTG+IG+ +I GF +L+ +P+P R +ALG ++ Sbjct: 127 GLFDWKYYVGNQLMSKTIGVLGTGEIGKRVIQIAHGFNMNVLSVTAHPSPERAKALGVKF 186 Query: 189 LALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALK 248 + LD LL+ESDIV+LH PLT +T H+I A+ LA MKP A+LINT RG +V AAL+EALK Sbjct: 187 VDLDTLLSESDIVTLHVPLTPETEHMIGARELAKMKPTAILINTARGKVVEEAALMEALK 246 Query: 249 SGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIA 308 ++ GLDV+E E PL D + LL NVV+T H AFL+ E+L Sbjct: 247 EKKIAGAGLDVFERE-----------PLSMD--SPLLEMHNVVLTPHIAFLSEESLDECT 293 Query: 309 DTTLDNIAAWQDGTPRNRV 327 +++N+ + G P+N V Sbjct: 294 YISIENVEMFAKGKPQNVV 312 Lambda K H 0.323 0.137 0.402 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: 243 Number of extensions: 5 Number of successful extensions: 3 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: 319 Length adjustment: 28 Effective length of query: 301 Effective length of database: 291 Effective search space: 87591 Effective search space used: 87591 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 48 (23.1 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