Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CA265_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase
Query= BRENDA::O66939 (334 letters) >FitnessBrowser__Pedo557:CA265_RS12240 Length = 311 Score = 152 bits (384), Expect = 1e-41 Identities = 98/325 (30%), Positives = 168/325 (51%), Gaps = 31/325 (9%) Query: 3 VLFTSVPQEDVPFYQEALKDLSLKIYTTDVSKVPENELKKAELISVFVYDK--LTEELLS 60 +L ++ +E + QE ++ ++T ++ L E+ ++ K + + L+ Sbjct: 6 LLLETIAEEALALLQE-----NVNVFTGYDEAGLKDTLNNVEVHAIITRGKKHIDKTLMD 60 Query: 61 KMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTLVKRLKRIE 120 P L++ VG D++D+D + I V + P + ++AEHT A++L L++ + R Sbjct: 61 ACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDMHRSV 120 Query: 121 DRVKKLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGLAFGMKVLCYDVVKREDLKE 180 + VK+ N++ ++ ELN TLG++G G IG RVA G AFGMKVLC+ Sbjct: 121 NHVKQNNWNWRNQYAGDELNGKTLGILGLGNIGKRVAKLGDAFGMKVLCW---------S 171 Query: 181 KGCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLINTARGKVVDTDAL 240 + LDE+L++SDV+SLH+P + ET+ +I +++LMK +LINTARG ++D AL Sbjct: 172 RSVQDLPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTARGALIDHAAL 231 Query: 241 YRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITPHIAYYTD 300 A G +G DV DE L+ L + N ++TPH A T Sbjct: 232 LDALNAGTIAGFAADVLPDE---------------PPLQSLAVVQHPNALVTPHAASLTA 276 Query: 301 KSLERIREETVKVVKAFVKGDLEQI 325 + +++ TV+ V + + G ++ Sbjct: 277 STYKQMCLLTVRNVLSVLAGQQPEL 301 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: 196 Number of extensions: 6 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: 334 Length of database: 311 Length adjustment: 28 Effective length of query: 306 Effective length of database: 283 Effective search space: 86598 Effective search space used: 86598 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: 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