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 203422 SO4344 threonine dehydratase (NCBI ptt file)
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__MR1:203422 Length = 545 Score = 183 bits (464), Expect = 1e-50 Identities = 103/295 (34%), Positives = 168/295 (56%), Gaps = 6/295 (2%) Query: 38 TPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGVVTHSSGNHA 97 TP+ S + A +G Q+F K E Q +FK+RGA N I L E +GVV S+GNHA Sbjct: 49 TPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHA 108 Query: 98 AAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVAKRVQEETGA 157 VA++A RG+ A IV+P P KVD V+R GG+++ + + A + ++ G Sbjct: 109 QGVAMSAASRGVDAVIVMPETTPDIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGR 168 Query: 158 ILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAAKAINPSIRILA 217 + + PF+++ I+GQGT++ E+L++ +++ I VP+ GGGLI+G+A KA+ P ++I+ Sbjct: 169 VYIAPFDDEAVIAGQGTIAQEMLQQQRDLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVG 228 Query: 218 AEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRDLVDDIIVVDDNAIV 276 EP+ A + AG+ +TL ADG+ +G + V + VD ++ V + I Sbjct: 229 VEPEDAACLKAAMEAGEPVTLSQVGLFADGVAVKRIGTEPFRVAKLCVDAVVTVTSDEIC 288 Query: 277 DAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHES---SKIGIIVSGGNVD 328 A+K +E + EP+GA+ LA ++ ++A ES K+ I+SG NV+ Sbjct: 289 AAVKDIFEDTRAIAEPAGALSLAGL--KKYVSTNATGESGRGEKVAAILSGANVN 341 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: 340 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: 545 Length adjustment: 32 Effective length of query: 307 Effective length of database: 513 Effective search space: 157491 Effective search space used: 157491 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: 51 (24.3 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