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_040638342.1 MICLODRAFT_RS08845 threonine/serine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_000262405.1:WP_040638342.1 Length = 313 Score = 182 bits (463), Expect = 7e-51 Identities = 111/312 (35%), Positives = 172/312 (55%), Gaps = 11/312 (3%) Query: 24 IREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDE 83 I A ARIAP++ +TPVL+ S G + K E Q AG+FK RGA N++ L + Sbjct: 8 IEAAHARIAPHIRRTPVLNMGSAFGHDGA-VSLKLEFLQHAGSFKTRGAFNTL--LSKEL 64 Query: 84 ASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIES 143 + GV S GNH AAVA AAK G+ A I +P + K+ ++ +G ++ Sbjct: 65 PAAGVAAASGGNHGAAVAYAAKQLGVKARIFVPEISSPAKIAVIRSHGAEVVIGGARYAD 124 Query: 144 RESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVA 203 ++ E+GA+ +HPF ++T+ GQGT +LE ++ P +DT++V + GGGLISGVA Sbjct: 125 AQAACDLYVAESGALRIHPFAAESTMIGQGTAALEWEQDAPALDTVLVAVGGGGLISGVA 184 Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262 ++++ EP+G+ S AG+ + + + AD L A GDL + + RD Sbjct: 185 SWWAG---RVKVVGVEPEGSRALHASLEAGRPVDVDVDSVAADSLGAKNTGDLVYSICRD 241 Query: 263 LVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGIIV 322 VD + +V D AI DA ++ + ++A EP GA LAA +S +K S ++G+++ Sbjct: 242 TVDHVALVTDAAIRDAQRLLWRDYRIASEPGGAAALAALVSGAYKPRS----GERVGVLL 297 Query: 323 SGGNVDLGVLWE 334 G NV+L L E Sbjct: 298 CGANVELAKLAE 309 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: 233 Number of extensions: 10 Number of successful extensions: 7 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: 313 Length adjustment: 28 Effective length of query: 311 Effective length of database: 285 Effective search space: 88635 Effective search space used: 88635 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