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 3609317 Dshi_2702 Pyridoxal-5'-phosphate-dependent protein beta subunit (RefSeq)
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__Dino:3609317 Length = 330 Score = 191 bits (486), Expect = 2e-53 Identities = 112/325 (34%), Positives = 179/325 (55%), Gaps = 11/325 (3%) Query: 18 AADIHSIREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIF 77 A D I+ A+AR+ +V +TP+LS+ ++DA+ G+++ K EC Q G+FK RG ++ Sbjct: 4 APDFDRIKAAEARLDGHVRRTPILSAPALDALAGRRVLVKAECLQHTGSFKARGGWAAVS 63 Query: 78 ALDDDEASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWS 137 AL ++GV+ SSGNHA VA AA G A IV+P +APA KV+N + G +++ Sbjct: 64 ALPAAVRARGVIACSSGNHAQGVARAAAAHGTRALIVMPGDAPAPKVENTRALGAEVVFY 123 Query: 138 DVSIESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVP----EIDTIIVPI 193 D + E R+ + + E G L+ P+++ I+GQ T LE+ + ++V Sbjct: 124 DRAREDRDGLTATLAERDGLTLIKPYDDTEVIAGQATTGLEIAAQAAAEGVHAAEVLVCC 183 Query: 194 SGGGLISGVALAAKAINPSIRILAAEPKGADDSAQSKAAG-KIITLPSTNTIADG-LRAF 251 GGGL +G+ALA P +R+ EP G DD A+S AAG ++ +I D L Sbjct: 184 GGGGLSAGIALALAETAPRMRVRPVEPDGFDDMARSLAAGTRLANSARDGSICDAILTPM 243 Query: 252 LGDLTWPVVRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSA 311 G++T+PV+ +VV + ++ MK+ ++ LK+ +EP GA+ LAAAL F+ + Sbjct: 244 PGEITFPVLASRAGPGLVVTEGEVLRTMKLAFQHLKLVLEPGGAVALAAAL---FRPDAL 300 Query: 312 WHESSKIGIIVSGGNVDLGVLWESL 336 + + +GGNV V +L Sbjct: 301 --SGDAVIAVATGGNVSAEVFARAL 323 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: 227 Number of extensions: 11 Number of successful extensions: 3 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: 330 Length adjustment: 28 Effective length of query: 311 Effective length of database: 302 Effective search space: 93922 Effective search space used: 93922 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: 49 (23.5 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