Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate GFF770 Psest_0784 L-serine dehydratase, iron-sulfur-dependent, single chain form
Query= uniprot:P33073 (292 letters) >FitnessBrowser__psRCH2:GFF770 Length = 458 Score = 132 bits (332), Expect = 1e-35 Identities = 90/278 (32%), Positives = 141/278 (50%), Gaps = 5/278 (1%) Query: 3 NTAREIIDVCNERGIKIYDLVLEEEI--KNSHTTEEEIRKKLDAVIDVMHASA-TKNLTQ 59 ++A +++ C + I +L+L E + T + + + D + A T+ + Sbjct: 175 HSAAQLLAHCTAHSLTISELMLANETVWRPQGETRAGLLRIWQVMQDCVEAGCRTEGVMP 234 Query: 60 SDVTEYKMIDGFAKRTYEYANSGKSIVGDFLAKAMAMAFSTSEVNASMGKIVAAPTAGSS 119 + + G ++ E+ + + L A + +E NAS G++V APT G++ Sbjct: 235 GGLKVRRRAAGLYRQLSEHPEANLRDALNVLDWVDLYALAVNEENASGGRVVTAPTNGAA 294 Query: 120 GIMPAMLVAATEKY-NFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAMA 178 GI+PA+L D + LT+ IG + + A+ +GAE GCQ E G A +M Sbjct: 295 GIIPALLHYYMRFVPGADEDGVVRFLLTAAAIGMLYKENASISGAEVGCQGEVGVACSMG 354 Query: 179 AAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADLA 238 A AL E+LGGT +Q +AA I + + LGL CDP+ GLVQ PC RNA G + A +A +A Sbjct: 355 AGALCEVLGGTPQQVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAVKAINAARMA 414 Query: 239 LAGVES-LVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 L G S + D+V+ M + G M +ET GGLA Sbjct: 415 LRGDGSHFISLDKVIRTMRQTGADMKSKYKETARGGLA 452 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: 234 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