Align L-lactate dehydrogenase; L-LDH; EC 1.1.1.27 (uncharacterized)
to candidate WP_020562043.1 A3OW_RS0103515 hypothetical protein
Query= curated2:B1LAF5 (319 letters) >NCBI__GCF_000372865.1:WP_020562043.1 Length = 329 Score = 206 bits (524), Expect = 6e-58 Identities = 111/308 (36%), Positives = 183/308 (59%), Gaps = 10/308 (3%) Query: 1 MKIGIVGLGRVGSSTAFALLMKGFAREMVLIDVDKKRAEGDALDLIHGTPFTRRANIYAG 60 MKIGI+G+G VGS+ A+ L++KG + +VL + + +A+GDALDL H F I Sbjct: 1 MKIGIIGMGHVGSTLAYGLVLKGLCKHLVLANRNVTKAQGDALDLQHTLSFCEHPIIIES 60 Query: 61 D-YADLKGSDVVIVAAGVPQKPGETRLQLLGRNARVMKEIARNVSKYAPDSIVIVVTNPV 119 ++ D++I+ A VP ++R++L N + KE+ +++ PD+I IV+TNPV Sbjct: 61 SRIEEVTACDILIMTASVPFAAMKSRIELGPANVALFKELIPDLAANNPDAIFIVITNPV 120 Query: 120 DVLTYFFLKESGMDPRKVFGSGTVLDTARLRTLIAQHCGFSPRSVHVYVIGEHGDSEVPV 179 +V+TY + SG KV G GT++D+AR R+L+++ P + Y++GEHG + PV Sbjct: 121 EVMTYLTYRLSGFSASKVLGIGTLVDSARFRSLLSRMEQIHPADLRAYILGEHGPHQFPV 180 Query: 180 WSGAMIGGIPLQNMCQICQKCDSKILENFAEKTKRAAYEIIERKGATHYAIALAVADIVE 239 +S A G QI +++L E A +E+ KG T+YAIA A ++++ Sbjct: 181 FSHASAGSE------QIVDNLPNRLL---CETVNNAGHEVYGLKGHTNYAIATAACEVIQ 231 Query: 240 SIFFDEKRVLTLSVYLEDYLGVKDLCISVPVTLGKHGVERILKLNLNEEELEAFRKSASI 299 +I +D+ R + LS+Y ++LG+K C S+PV +G+ GV R L+ +LN E +A +A++ Sbjct: 232 AIVYDDHRTMPLSLYFNEWLGIKKNCFSIPVVVGRAGVTRYLRPDLNLLEQQALATTAAL 291 Query: 300 LKNAINEI 307 +K IN + Sbjct: 292 VKANINRL 299 Lambda K H 0.320 0.137 0.392 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: 229 Number of extensions: 13 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: 319 Length of database: 329 Length adjustment: 28 Effective length of query: 291 Effective length of database: 301 Effective search space: 87591 Effective search space used: 87591 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