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_044048880.1 RCA23_RS02360 threonine/serine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_000738435.1:WP_044048880.1 Length = 309 Score = 142 bits (357), Expect = 1e-38 Identities = 96/304 (31%), Positives = 155/304 (50%), Gaps = 14/304 (4%) Query: 24 IREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDE 83 + A RI P+V +TPVL + + G L K E Q G+FK RGA NS+ ++D + Sbjct: 7 VSHAWTRIKPHVLRTPVLETD----VFGMPLTLKLEQLQHTGSFKARGAMNSLLSMDVPK 62 Query: 84 ASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIES 143 A G+V S GNH AAVA AA G A I +P A K++ ++ G ++ + + Sbjct: 63 A--GLVAASGGNHGAAVAWAAARLGHRARIYVPELAGDAKINLIQSLGADLVVVPGAYAN 120 Query: 144 RESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVA 203 A ++++GA +H F+ T++GQGTV E E+ DT+++ + GGGLI G Sbjct: 121 ALEQALSYEKDSGAAQIHAFDAPGTVAGQGTVMAEWEEQGLMADTVLIAVGGGGLIGG-- 178 Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262 A + +++ EP A Q+ G T+ + A+ L A G + + + R Sbjct: 179 -AMAWLEGRRKLVGVEPFNAPTLTQALEHGPQTTVEVSGLAANALGAKQAGRICYDLARA 237 Query: 263 LVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGIIV 322 + + V+D AI DA K + L++ VEP+GA LAA LS ++ + ++ +++ Sbjct: 238 TGTNCVNVEDEAIADAQKRLWTALRLVVEPAGAAALAALLSGAYRP----QKDERLAVLL 293 Query: 323 SGGN 326 G N Sbjct: 294 CGAN 297 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: 214 Number of extensions: 12 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: 309 Length adjustment: 28 Effective length of query: 311 Effective length of database: 281 Effective search space: 87391 Effective search space used: 87391 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