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 Ac3H11_2042 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2042 Length = 519 Score = 168 bits (425), Expect = 3e-46 Identities = 101/308 (32%), Positives = 167/308 (54%), Gaps = 13/308 (4%) Query: 29 ARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGV 88 AR+ ++ + + S+ + ++ K E Q +FK+RGA N + L ++ +GV Sbjct: 17 ARVYDVAVESALEPAKSLSRRLHNKVLLKREDQQPVFSFKLRGAYNKMAHLTPEQLQRGV 76 Query: 89 VTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVA 148 + S+GNHA VA++A G A +V+P P KVD VK GG ++ S A Sbjct: 77 ICASAGNHAQGVAMSAHKLGTRAVVVMPTTTPQLKVDAVKTLGGEVVLHGESYSDAYEHA 136 Query: 149 KRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVP-----EIDTIIVPISGGGLISGVA 203 R+Q+E G VHPF++ I+GQGT+++E+L ++ ++D + V I GGGL+SGVA Sbjct: 137 ARLQKEQGLTFVHPFDDPLVIAGQGTIAMEILRQLQSLGSNQLDAVFVAIGGGGLVSGVA 196 Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262 KA+ P I+++ + +D QS A + +TLP +DG +G+ T+ V + Sbjct: 197 NYIKAVRPEIKVIGVQMNDSDAMIQSVNAHQRVTLPDVGLFSDGTAVKLVGEETFRVAQG 256 Query: 263 LVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHES--SKIGI 320 LVD+ + VD +A+ A+K + + VEP+GA+ +AA KQ A H++ Sbjct: 257 LVDEFVTVDTDAVCAAIKDIFVDTRSIVEPAGALAVAA-----IKQYVATHKTKGETYAA 311 Query: 321 IVSGGNVD 328 I+ G N++ Sbjct: 312 ILCGANMN 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: 304 Number of extensions: 10 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: 519 Length adjustment: 32 Effective length of query: 307 Effective length of database: 487 Effective search space: 149509 Effective search space used: 149509 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