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_086510351.1 BZY95_RS13015 threonine/serine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_002151265.1:WP_086510351.1 Length = 315 Score = 187 bits (474), Expect = 4e-52 Identities = 109/308 (35%), Positives = 172/308 (55%), Gaps = 6/308 (1%) Query: 21 IHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALD 80 + I+EAQ RIA + TP+L + G++++ K E FQ+ G+FK RG N + + Sbjct: 4 LERIQEAQRRIADSLPPTPLLLDHVLSEKFGRRIWLKGELFQRTGSFKPRGGLNWLRSAG 63 Query: 81 DDEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVS 140 ++E + G+ S+GNHA +A AA +P IV+P NA KV+ ++ G +I Sbjct: 64 EEELAGGLGAVSAGNHALGLAWAAGQADVPVTIVMPENASPFKVEGSRKLGAEVILHGDI 123 Query: 141 IESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLIS 200 E+ E + R+ E G LVHP++++ ++GQGTV LE+LE+ PE I+ P+ GGGLI+ Sbjct: 124 NEAWE-LMHRLVAERGLTLVHPYDDERIMAGQGTVGLEILEQAPEATAILCPVGGGGLIA 182 Query: 201 GVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGL-RAFLGDLTWPV 259 G+ AA A+ P + ++ EP GA A + +AG L T A L A +G+ T+PV Sbjct: 183 GIGSAAAALRPGLALIGVEPSGAASMAAAWSAGAPERLERVATCAKSLGAAIVGEHTYPV 242 Query: 260 VRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIG 319 R+ ++ VDD+AI AM+ K+ EP A+G+AA L D + Sbjct: 243 CRETTQKLLQVDDDAIGRAMRHLLYQAKLMAEPGAAVGVAALLED----LVTLPPEGDVV 298 Query: 320 IIVSGGNV 327 ++++GGN+ Sbjct: 299 VVITGGNM 306 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: 249 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: 339 Length of database: 315 Length adjustment: 28 Effective length of query: 311 Effective length of database: 287 Effective search space: 89257 Effective search space used: 89257 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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