Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate 16881 b2797 L-serine deaminase II (NCBI)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__Keio:16881 Length = 455 Score = 129 bits (325), Expect = 9e-35 Identities = 94/280 (33%), Positives = 144/280 (51%), Gaps = 10/280 (3%) Query: 3 NTAREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDV 62 ++A ++ C E G+ + L+++ E+ + ++EE+ + L V +VM + ++ V Sbjct: 172 SSAADLQKHCQETGLSLSGLMMKNEL--ALHSKEELEQHLANVWEVMRGGIERGISTEGV 229 Query: 63 TEYKM-IDGFAKRTYEYANSGKSIVGDFLAKA---MAMAFSTSEVNASMGKIVAAPTAGS 118 K+ + A S D +A A + +E NA+ G++V APT G+ Sbjct: 230 LPGKLRVPRRAAALRRMLVSQDKTTTDPMAVVDWINMFALAVNEENAAGGRVVTAPTNGA 289 Query: 119 SGIMPAMLVAATEKY--NFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASA 176 GI+PA+L A +K+ + ++ L + IG + A+ +GAE GCQ E G A + Sbjct: 290 CGIIPAVL-AYYDKFIREVNANSLARYLLVASAIGSLYKMNASISGAEVGCQGEVGVACS 348 Query: 177 MAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISAD 236 MAAA L E+LG + Q AA I + + LGL CDP+AG VQ PC RNA + A +A Sbjct: 349 MAAAGLAELLGASPAQVCIAAEIAMEHNLGLTCDPVAGQVQVPCIERNAIAAVKAVNAAR 408 Query: 237 LALAGV-ESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 +AL E V D+V+ M E G M RET GGLA Sbjct: 409 MALRRTSEPRVCLDKVIETMYETGKDMNAKYRETSRGGLA 448 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: 288 Number of extensions: 7 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