Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_085544045.1 B9Y55_RS03840 hydroxyacid dehydrogenase
Query= BRENDA::Q9I530 (329 letters) >NCBI__GCF_900177735.1:WP_085544045.1 Length = 316 Score = 162 bits (409), Expect = 1e-44 Identities = 103/306 (33%), Positives = 159/306 (51%), Gaps = 17/306 (5%) Query: 23 HGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPVLERLAAGGTRLVALRSAGYNHV 82 H FE + + ++ + LA + A N L V+ + +++++ GY+HV Sbjct: 28 HSFEAYCRSDDVKENVKRLAGADVAIIA--NMPLGGQVIS--SCDRLKMISVAFTGYDHV 83 Query: 83 DLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHGLTGFDL 142 D+ + + + V + YS +V E A+GL L + R++ R G + GL G L Sbjct: 84 DMESCLSKRITVSNCAGYSTDSVVELALGLSLAVVRKIVPCDGAVRAGK-TKDGLIGNQL 142 Query: 143 HGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPRIQALGGRYLALDALLAESDIVS 202 GK VG++GTG IG A + GC ++AY + ++G YL+L L++ D++S Sbjct: 143 AGKTVGIVGTGAIGVKVAAVFKALGCNVVAYSRSQRDEVLSMGIPYLSLKDLMSSCDLIS 202 Query: 203 LHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLGLDVYEE 262 LH P +T LID +++MK + LINT RG +V+ AL +ALKSG + G+DV++ Sbjct: 203 LHLPCNGETAGLIDRDMISSMKRSSFLINTARGPIVDNKALADALKSGSIAGAGIDVFDM 262 Query: 263 EADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIAAWQDGT 322 E PL + LL PN V+T H AF T EAL + A +DN+ W DG Sbjct: 263 E----------PPLLEGY--PLLDAPNCVLTPHVAFATPEALQSRAVIAIDNVRLWMDGK 310 Query: 323 PRNRVR 328 P+N VR Sbjct: 311 PQNVVR 316 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: 239 Number of extensions: 12 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: 316 Length adjustment: 28 Effective length of query: 301 Effective length of database: 288 Effective search space: 86688 Effective search space used: 86688 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 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