Align Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 (characterized)
to candidate WP_011840691.1 RSPH17029_RS04715 threonine/serine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_000015985.1:WP_011840691.1 Length = 325 Score = 206 bits (525), Expect = 5e-58 Identities = 118/316 (37%), Positives = 184/316 (58%), Gaps = 11/316 (3%) Query: 19 ADIHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFA 78 +DI I A AR+A + +TP+LSS +D I G+++ K EC Q G+FK RG +++ A Sbjct: 2 SDIAMIEAAAARLAGHARRTPLLSSPFLDEIAGRRVLVKAECLQHTGSFKFRGGWSALSA 61 Query: 79 LDDDEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSD 138 L+ ++GV+ +SSGNHA VALAA G PA IV+P +AP K++N + G ++ D Sbjct: 62 LEPARRAQGVIAYSSGNHAQGVALAAARHGAPAVIVMPADAPQLKIENTRALGAEVVLYD 121 Query: 139 VSIESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDT----IIVPIS 194 + E R+++ R+ +E G L+ PF+ I+GQGT LE+ E+ E ++ Sbjct: 122 RATEDRDAIGARLADERGLTLIRPFDEPLVIAGQGTTGLEIAEQAAEEGVTSADVLTCCG 181 Query: 195 GGGLISGVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPS-TNTIADGL-RAFL 252 GGGL +G+ALA +A P +R+ EP G DD+A+S AAG+I + + + +I D + Sbjct: 182 GGGLTAGIALALEARAPGLRVRPVEPVGFDDTARSLAAGEIRSNAALSGSICDAIVTPQP 241 Query: 253 GDLTWPVVRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAW 312 G +T+P++ L + V D + AM + + LK+ +EP GA+ LAAAL F+ + Sbjct: 242 GRITFPILARLCGPGLAVTDAEALRAMALAFLRLKIVLEPGGAVALAAAL---FRPEAL- 297 Query: 313 HESSKIGIIVSGGNVD 328 + + SGGNVD Sbjct: 298 -DGDAVICTASGGNVD 312 Lambda K H 0.316 0.133 0.381 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: 230 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: 339 Length of database: 325 Length adjustment: 28 Effective length of query: 311 Effective length of database: 297 Effective search space: 92367 Effective search space used: 92367 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. 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