Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate Ac3H11_929 L-serine dehydratase (EC 4.3.1.17)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_929 Length = 466 Score = 126 bits (316), Expect = 1e-33 Identities = 93/284 (32%), Positives = 143/284 (50%), Gaps = 19/284 (6%) Query: 4 TAREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVT 63 T E++ C G+ L+ E + E+R++L A+ M + + + Sbjct: 184 TGAELLAQCQATGLTPAQLMAANE--QHWRSASEVRRQLMAIWKTMAGAVQRGCASTGTL 241 Query: 64 EYKMIDGFAKRTYEYANSGKSIVGDFLAKAMAM-------AFSTSEVNASMGKIVAAPTA 116 M +R E + S L ++M A + +E NA+ G++V APT Sbjct: 242 PGPM--HVRRRAAELHHKLSSAPEAALRDPLSMLDWVNLYAMAVNEENAAGGRVVTAPTN 299 Query: 117 GSSGIMPAMLVAATEKYNFDRTTIQNGF----LTSIGIGQVITKYATFAGAEGGCQAECG 172 G++G++PA+L NF ++G LT+ IG + + A+ +GAE GCQ E G Sbjct: 300 GAAGVIPAVLHYYV---NFLPGANEDGIATFLLTAGAIGIIYKENASLSGAEVGCQGEVG 356 Query: 173 SASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAF 232 A +MAA AL ++GG+ EQ +AA I + + LG+ CDP+ GLVQ PC RNA G I A Sbjct: 357 VACSMAAGALAAVMGGSPEQIENAAEIGMEHNLGMTCDPVGGLVQIPCIERNAMGAIKAI 416 Query: 233 ISADLALAG-VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 +A +AL G + +V D+V+ M + G M +ET GGLA Sbjct: 417 NAARMALRGDGQHVVSLDKVIKTMMQTGADMKVKYKETSRGGLA 460 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: 253 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: 466 Length adjustment: 30 Effective length of query: 262 Effective length of database: 436 Effective search space: 114232 Effective search space used: 114232 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