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 5207772 Shew_0293 threonine dehydratase (RefSeq)
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__PV4:5207772 Length = 516 Score = 182 bits (463), Expect = 1e-50 Identities = 108/298 (36%), Positives = 169/298 (56%), Gaps = 17/298 (5%) Query: 38 TPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGVVTHSSGNHA 97 TP+ S + A +G Q+F K E Q +FK+RGA N I L +E +GVV S+GNHA Sbjct: 32 TPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAELSQEECQRGVVCASAGNHA 91 Query: 98 AAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVAKRVQEETGA 157 VA++A RG+ A IV+P+ P KVD V+R GG ++ S + A+++ + G Sbjct: 92 QGVAMSASARGVSAVIVMPQTTPDIKVDAVRRLGGTVVLYGQSFDMANEHAQQLARDEGR 151 Query: 158 ILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAAKAINPSIRILA 217 I V PF+++ I+GQGTV+ E+L++ +++ + VP+ GGGLI+G+A KA+ P ++I+ Sbjct: 152 IYVAPFDDEAVIAGQGTVAQEMLQQQRDLEVVFVPVGGGGLIAGIAAYYKAVMPQVKIIG 211 Query: 218 AEPKGADDSAQSKA---AGKIITLPSTNTIADGLRA-FLGDLTWPVVRDLVDDIIVVDDN 273 EP +DSA KA A + + L ADG+ +G + + R+ VD ++ V + Sbjct: 212 VEP---EDSACLKAALEADERVVLSQVGLFADGVAVKQIGAEPFRLAREYVDQVVTVTSD 268 Query: 274 AIVDAMKMCYEMLKVAVEPSGAIGLAAA---LSDEFKQSSAWHESSKIGIIVSGGNVD 328 I A+K +E + EP+GA+ LA + DE K K+ I+SG NV+ Sbjct: 269 EICAAVKDIFEDTRAIAEPAGALSLAGLKKYIGDEGK-------GQKVAAILSGANVN 319 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: 313 Number of extensions: 16 Number of successful extensions: 2 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: 516 Length adjustment: 32 Effective length of query: 307 Effective length of database: 484 Effective search space: 148588 Effective search space used: 148588 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: 50 (23.9 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