Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate 5208228 Shew_0740 L-serine dehydratase 1 (RefSeq)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__PV4:5208228 Length = 455 Score = 133 bits (334), Expect = 9e-36 Identities = 96/283 (33%), Positives = 142/283 (50%), Gaps = 20/283 (7%) Query: 5 AREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNL-TQSDVT 63 A E++D+C E G+ I +++ E + +E I + +AV M + + T+ + Sbjct: 173 AEELLDLCQETGMSISAIMMANE--RALHSEAHIAEGFEAVWHTMKEAIERGCHTEGVLA 230 Query: 64 EYKMIDGFAKRTYEYANSGKSIVGD---FLAKAMAMAFSTSEVNASMGKIVAAPTAGSSG 120 + A + +G+ + D + A + SE NA+ G++V +PT G++G Sbjct: 231 GPLRVPRRAPALFRQLATGERLSADPMMIVDWVNMFALAVSEENAAGGRVVTSPTNGAAG 290 Query: 121 IMPAMLVAATEKYNFDRTTIQNG-------FLTSIGIGQVITKYATFAGAEGGCQAECGS 173 I+PA+L FD+ G FL + IG + + A+ +GAE GCQ E G Sbjct: 291 IIPAVLAY------FDKFIQPVGPKEYSRYFLAAAAIGGLYKRNASISGAEVGCQGEVGV 344 Query: 174 ASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFI 233 A +MAAA L E++GG Q AA I + + LGL CDP+AG VQ PC RNA + A Sbjct: 345 ACSMAAAGLAELMGGNPAQVCIAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAIN 404 Query: 234 SADLAL-AGVESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 SA +AL E V D+V+ M E G M RET GGLA Sbjct: 405 SARMALRRNSEPRVSLDKVIATMYETGKDMHVKYRETSQGGLA 447 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: 267 Number of extensions: 14 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: 455 Length adjustment: 29 Effective length of query: 263 Effective length of database: 426 Effective search space: 112038 Effective search space used: 112038 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