Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate PfGW456L13_1089 L-serine dehydratase (EC 4.3.1.17)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089 Length = 458 Score = 138 bits (348), Expect = 2e-37 Identities = 95/290 (32%), Positives = 151/290 (52%), Gaps = 24/290 (8%) Query: 3 NTAREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDV 62 ++A E++++C + +++ +L++ E +E+EIR L + M + L + Sbjct: 174 SSAAELLELCKKHNLRVAELMMANE--RVWRSEDEIRSGLMKLWRAMQDCVEQGLKHEGI 231 Query: 63 T----EYKMIDGFAKRTYEYANSGKSIVGDFLAK---AMAMAFSTSEVNASMGKIVAAPT 115 + R+ + N +++G L+ A + +E NA+ G++V APT Sbjct: 232 LPGGLNVRRRAAKLHRSLQELNK-PNVIGSTLSAMEWVNLFALAVNEENAAGGRMVTAPT 290 Query: 116 AGSSGIMPAML-------VAATEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQ 168 G++GI+PA+L A T+ + + FL + +G + K A+ +GAE GCQ Sbjct: 291 NGAAGIIPAVLHYFMKFSEAVTD------ANVVDYFLGAAAVGILCKKNASISGAEVGCQ 344 Query: 169 AECGSASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGV 228 E GSA AMAAA L E+LG T EQ +AA I + + LGL CDP+ GLVQ PC RNA Sbjct: 345 GEVGSACAMAAAGLAEILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAA 404 Query: 229 INAFISADLALAG-VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLAGS 277 + A +A +AL G + + D V+ M + G M + +ET GGLA S Sbjct: 405 VKAINAAQMALRGDGQHFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS 454 Lambda K H 0.317 0.132 0.361 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: 246 Number of extensions: 11 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: 292 Length of database: 458 Length adjustment: 30 Effective length of query: 262 Effective length of database: 428 Effective search space: 112136 Effective search space used: 112136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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