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 GFF3574 PGA1_c36290 putative phenylserine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__Phaeo:GFF3574 Length = 314 Score = 135 bits (340), Expect = 1e-36 Identities = 93/307 (30%), Positives = 157/307 (51%), Gaps = 14/307 (4%) Query: 24 IREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDE 83 IR A RI PY+ +TP+L +T + + K E Q G+FK RGA N++ + Sbjct: 7 IRAADTRIRPYIQRTPILETTGFG--LDYPISLKLEHMQHTGSFKARGAFNTLLGGSVPD 64 Query: 84 ASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIES 143 A G+V S GNH AAVA AAK G+ A + +P A K+ ++ G + + + Sbjct: 65 A--GLVAASGGNHGAAVAYAAKRLGMRARVYVPEMAGPAKIALIRACGADLKVVPGAYAN 122 Query: 144 RESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVA 203 A+ +++TGA+ VH ++ T+ GQGT E + E DT+++ + GGGLI+G Sbjct: 123 ALEQAQAYEQQTGAMQVHAYDAAATVIGQGTCFAEWDAQGLEADTLLIAVGGGGLIAG-- 180 Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262 A S +I+A EP+ + + A G+ + + + A+ L A +G L + + + Sbjct: 181 -AMAWYGGSKKIVAVEPETSSALNAALAVGRPVDVEVSGVAANALGARRIGTLCYELAQG 239 Query: 263 LVDDI--IVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGI 320 D + + V D AI A ++ ++ VEP+GA LAA S ++ + ++ + Sbjct: 240 QSDTVTSLTVSDEAISAAQNKLWKERRLLVEPAGATALAALTSGAYQPA----PDERVAV 295 Query: 321 IVSGGNV 327 ++ GGN+ Sbjct: 296 LLCGGNI 302 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: 229 Number of extensions: 10 Number of successful extensions: 6 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: 314 Length adjustment: 28 Effective length of query: 311 Effective length of database: 286 Effective search space: 88946 Effective search space used: 88946 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 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