Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate 201398 SO2248 L-serine dehydratase 1 (NCBI ptt file)
Query= uniprot:P33073 (292 letters) >FitnessBrowser__MR1:201398 Length = 458 Score = 143 bits (361), Expect = 6e-39 Identities = 98/279 (35%), Positives = 147/279 (52%), Gaps = 8/279 (2%) Query: 3 NTAREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDV 62 N++ +++++C E G+ I L++ E+ S +EEE++ KL + M + + + Sbjct: 176 NSSAQLLELCTEHGLSISSLMMANEL--SLASEEEVKAKLWNIWQTMKTCIERGYQKEGI 233 Query: 63 TEYKM-IDGFAKRTYEYANS-GKSIVGDFLAKAMA--MAFSTSEVNASMGKIVAAPTAGS 118 + + A Y + G++ V A A S +E NA+ ++V APT G+ Sbjct: 234 LPGGLKLRRRAPALYRRLKAEGRNNVDPLTAMDWVDLFALSVNEQNAAGDRVVTAPTNGA 293 Query: 119 SGIMPAMLVAA-TEKYNFDRTTIQNGFLTSIGIGQVITKYATFAGAEGGCQAECGSASAM 177 +GI+PA+L T D LT+ IG + K A+ +GAE GCQ E G A +M Sbjct: 294 AGIIPAVLCYYDTFVQEVDIDVCARYLLTAAAIGILYKKNASISGAEVGCQGEVGVACSM 353 Query: 178 AAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYPCTFRNASGVINAFISADL 237 AA AL E++GGTVE +AA I + + LGL CDP+ GLVQ PC RNA G I A ++ + Sbjct: 354 AAGALTEIMGGTVEHVENAAEIGMEHNLGLTCDPVGGLVQVPCIERNAMGAIKAINASRM 413 Query: 238 ALAG-VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 AL G V D+V+ M + G M +ET GGLA Sbjct: 414 ALRGDGNHKVSLDKVIKTMMDTGKDMRSKYKETAKGGLA 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: 265 Number of extensions: 10 Number of successful extensions: 4 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