Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_079557862.1 CDL62_RS17635 hydroxyacid dehydrogenase
Query= BRENDA::O66939 (334 letters) >NCBI__GCF_002201795.1:WP_079557862.1 Length = 334 Score = 161 bits (407), Expect = 2e-44 Identities = 98/283 (34%), Positives = 158/283 (55%), Gaps = 27/283 (9%) Query: 45 LISVFVYDKLTEELLSKMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEH 104 L+SVF +K+TEE++SK P+LKLI VG+D++D+DY +GI+VT+ P+ E AE Sbjct: 48 LVSVFG-NKVTEEMMSKAPKLKLIANYGVGYDNVDVDYATSQGIVVTNTPSPVTEPTAEL 106 Query: 105 TFAMILTLVKRLKRIEDRVKKLNFSQDS--EILARELNRLTLGVIGTGRIGSRVAMYGLA 162 ++L L + + + + + + + + + L+ L TLG+IG G IG +A A Sbjct: 107 AMLLMLALARNIIGLHNGILENSLPEWNVRNNLSTTLYNKTLGIIGMGAIGQALARRAKA 166 Query: 163 FGMKVL-----CYDVVKREDLKEKGCVYTSLDELLKESDVISLHVPYTKETHHMINEERI 217 FGMK++ C D E + Y S ELL++SD +S+HVP+++ET+H+I +E + Sbjct: 167 FGMKIIYHNRACLDSAIEEKYE---ATYVSKTELLQKSDYVSIHVPFSQETYHLIGKEEL 223 Query: 218 SLMKDGVYLINTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKN 277 LMK+ +LINT+RGKV+ L +A + + +G GLDVF +E I+ D Sbjct: 224 KLMKNSAFLINTSRGKVIHEKVLIKALKNREIAGAGLDVFSNEPIV----------PD-- 271 Query: 278 LKILELACKDNVIITPHIAYYTDKSLERIREETVKVVKAFVKG 320 EL V++TPH+ T ++ + + V+ F G Sbjct: 272 ----ELKNSPYVVLTPHVGSGTHEARAEMSQFVADVISNFFNG 310 Lambda K H 0.319 0.138 0.383 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: 279 Number of extensions: 9 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 334 Length of database: 334 Length adjustment: 28 Effective length of query: 306 Effective length of database: 306 Effective search space: 93636 Effective search space used: 93636 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 (21.7 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