Align L-serine dehydratase, alpha chain; Short=SDH; EC 4.3.1.17 (characterized, see rationale)
to candidate CA265_RS21785 CA265_RS21785 L-serine ammonia-lyase
Query= uniprot:P33073 (292 letters) >FitnessBrowser__Pedo557:CA265_RS21785 Length = 475 Score = 136 bits (342), Expect = 1e-36 Identities = 101/298 (33%), Positives = 149/298 (50%), Gaps = 36/298 (12%) Query: 5 AREIIDVCNERGIKIYDLVLEEEIKNSHTTEEEIRKKLDAVIDVMHASATKNLTQSDVTE 64 A++++ C G+K+ ++V+E E+ + TE E +K + + H + + Sbjct: 177 AKDLLHWCLSTGLKVSEIVMENEL--AWRTEAETKKGI-----LQHFAVMSDCIYRGCHT 229 Query: 65 YKMIDG---FAKRTYEYANS--GKSIVGDFLAKAMAM-----------------AFSTSE 102 + G A+R + GKS D+ + A+ A + +E Sbjct: 230 TGFLPGGLNVARRAFPLNKRLIGKSEYSDYNSWVEAIRKGGNGFNYTLDWVSCFALAVNE 289 Query: 103 VNASMGKIVAAPTAGSSGIMPAML---VAATEKYNFDRTTIQNGFLTSIGIGQVITKYAT 159 NAS G++V APT G++G++PA+L + + Y+ ++ I + IG + K AT Sbjct: 290 ENASFGRVVTAPTNGAAGVIPAVLQYFITFCDGYSEEK--IMQFIACASEIGSIFKKGAT 347 Query: 160 FAGAEGGCQAECGSASAMAAAALVEMLGGTVEQALHAASITIINVLGLVCDPIAGLVQYP 219 + A GGCQAE G +SAMAAAAL E LGG+ Q L AA I + + LGL CDPI GLVQ P Sbjct: 348 ISAAMGGCQAEIGVSSAMAAAALTECLGGSQRQVLMAAEIAMEHHLGLTCDPIGGLVQIP 407 Query: 220 CTFRNASGVINAFISADLALAG--VESLVPFDEVVIAMGEVGNSMIEALRETGLGGLA 275 C RN G I A ++ LAL ++ V D VV M E M +ET GGLA Sbjct: 408 CIERNTMGAIKAITASQLALQSNPDKAKVSLDAVVNTMWETALDMNAKYKETSDGGLA 465 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: 229 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 292 Length of database: 475 Length adjustment: 30 Effective length of query: 262 Effective length of database: 445 Effective search space: 116590 Effective search space used: 116590 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