Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate 8499231 DvMF_0011 serine dehydratase alpha chain (RefSeq)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__Miya:8499231 Length = 459 Score = 150 bits (380), Expect = 4e-41 Identities = 98/267 (36%), Positives = 136/267 (50%), Gaps = 3/267 (1%) Query: 14 ERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTEYKM-IDGFA 72 E G+ I++L+LE E+ + I +L A+I++M AS + + + + A Sbjct: 189 ETGLTIHELILENEMAVTGMGRAAILDRLAAIIELMEASVRRGIEDGGPLPGTLGVHRKA 248 Query: 73 KRTYEYANSGKSIVGDFLAKAMAMAFSTSEVNASMGKIVAAPTAGSSGIMPAMLVAATEK 132 + A + V FL + A AF+ +E NA+ G IV APT G++G+MPA+L A Sbjct: 249 RVLLMRAQRLPNEVDVFLGRLNAYAFAAAEENAAGGVIVTAPTCGAAGVMPALLYAMRHD 308 Query: 133 YNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAMAAAALVEMLGGTVEQ 192 ++ G L S +G + A AGAE GCQ E G ASAMAAA L G V Sbjct: 309 LAIGDRAVREGVLASAAVGFLAKHNAGIAGAEVGCQGEVGVASAMAAAMLAHARGNPVHV 368 Query: 193 ALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADLALA--GVESLVPFDE 250 +AA I + + LGL CDP+ G VQ PC RNA G + A+ + LA V D Sbjct: 369 VENAAEIALEHHLGLTCDPVGGYVQIPCIERNAVGAVKAYNACLLATCEDPRHHRVTLDS 428 Query: 251 VVIAMGEVGNSMIEALRETGLGGLAGS 277 V+ AM E+G M +ET GGLA S Sbjct: 429 VIAAMAEIGRDMNAKFKETSSGGLAVS 455 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: 228 Number of extensions: 13 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: 459 Length adjustment: 30 Effective length of query: 262 Effective length of database: 429 Effective search space: 112398 Effective search space used: 112398 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