Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate Echvi_0600 Echvi_0600 L-serine dehydratase, iron-sulfur-dependent, alpha subunit
Query= uniprot:P33073 (292 letters) >FitnessBrowser__Cola:Echvi_0600 Length = 302 Score = 204 bits (519), Expect = 2e-57 Identities = 114/279 (40%), Positives = 163/279 (58%), Gaps = 3/279 (1%) Query: 10 DVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTEYKMID 69 + C + + +Y V+E E +EE+I + L + VM + L + V+ MI+ Sbjct: 13 EYCEAKNVPLYAPVMEYEKDQRGKSEEQIWEGLRSAYKVMKDAVETGLKEEMVSRSGMIN 72 Query: 70 GFAKRTYEYANSGKSIVGDFLAKAMAMAFSTSEVNASMGKIVAAPTAGSSGIMPAMLVAA 129 AK+ Y + S++ + ++ A + EVN+ MG++VAAPTAG+SGI+P L Sbjct: 73 NGAKKVYHHP---LSVLSPEFQRLISRALAAKEVNSCMGRVVAAPTAGASGILPGTLYTL 129 Query: 130 TEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAMAAAALVEMLGGT 189 E + + G L G+ +I + A+ AGA GGCQAE GSA+AMA+ A+V LGG Sbjct: 130 QEIHGLSDDKVLEGLLIGAGVALIIEQNASLAGAVGGCQAETGSAAAMASGAMVYCLGGN 189 Query: 190 VEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADLALAGVESLVPFD 249 +Q +A +ITI +LGLVCDP+AGLV+ PC RNAS A SA +ALA V ++P D Sbjct: 190 TDQVFNAVAITIQCMLGLVCDPVAGLVEIPCVVRNASAAAIANSSAQIALADVSGVIPVD 249 Query: 250 EVVIAMGEVGNSMIEALRETGLGGLAGSKTGQKIRRDFL 288 E V AMGE+G SM +ET LGGLA + TG+ I + L Sbjct: 250 ECVEAMGEIGASMENKYKETALGGLAATLTGKGIAKKVL 288 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: 201 Number of extensions: 6 Number of successful extensions: 2 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: 302 Length adjustment: 26 Effective length of query: 266 Effective length of database: 276 Effective search space: 73416 Effective search space used: 73416 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: 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