Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 8499437 DvMF_0209 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::Q9I530 (329 letters) >FitnessBrowser__Miya:8499437 Length = 322 Score = 158 bits (399), Expect = 2e-43 Identities = 99/264 (37%), Positives = 142/264 (53%), Gaps = 19/264 (7%) Query: 72 VALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGD 131 + + + GY+ VD+ AA A +PV +VP Y AVA+H +L L RR+ R + G+ Sbjct: 69 IGVLATGYDVVDIRAAAARSIPVCNVPGYGTEAVAQHVFAFLLELCRRIARHDASVKVGN 128 Query: 132 FSLHG------LTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQALG 185 +S + T +L GK +G++G G +G+ +I FG ++LAY P Sbjct: 129 WSANKDWCFWETTQIELTGKAMGIVGFGNMGKRVGQIANAFGMKVLAYSPNTRTMPGYEP 188 Query: 186 GRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIE 245 Y++LD L A SD+V+LHCPLT TR +++ RLA+MK GA+LINT RG L++ AA+ Sbjct: 189 FAYVSLDELFARSDVVTLHCPLTDATRGMVNRVRLASMKQGAILINTARGPLLDEAAVAA 248 Query: 246 ALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALA 305 AL LG LG+DV E R D P LL+ N ++T H A+ T A Sbjct: 249 ALNDNHLGGLGVDVVAVE-----PIRPDNP--------LLTAKNCLITPHLAWATLTARQ 295 Query: 306 AIADTTLDNIAAWQDGTPRNRVRA 329 + T NI A+ G P N V+A Sbjct: 296 TLMRVTAGNIRAFLAGAPTNVVKA 319 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: 294 Number of extensions: 20 Number of successful extensions: 5 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: 322 Length adjustment: 28 Effective length of query: 301 Effective length of database: 294 Effective search space: 88494 Effective search space used: 88494 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 Sep 17 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