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 N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase
Query= SwissProt::Q7XSN8 (339 letters) >FitnessBrowser__Dyella79:N515DRAFT_0565 Length = 523 Score = 173 bits (439), Expect = 8e-48 Identities = 106/311 (34%), Positives = 175/311 (56%), Gaps = 12/311 (3%) Query: 25 REAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEA 84 R AR+ +T + S+ + A +G+++ K E Q +FK+RGA N + LD + Sbjct: 21 RTLAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLDAAQR 80 Query: 85 SKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGG---HIIWSDVSI 141 ++GV+ S+GNHA VALAA G+ A IV+P AP K+D V+R GG ++ + S Sbjct: 81 ARGVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGAWVEVVLAGDSY 140 Query: 142 ESRESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVP-EIDTIIVPISGGGLIS 200 ++ A R++++ G VHPF++ I+GQ TV +E+L + P + + VP+ GGGL++ Sbjct: 141 SDAQAEAARLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGGGLLA 200 Query: 201 GVALAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPV 259 GVA KA+ P ++++ + +D AQS G+ +TL ADG +G T+ + Sbjct: 201 GVAAYIKALRPEVKVIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAETFAL 260 Query: 260 VRDLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWH--ESSK 317 + VD ++ VD +AI A++ ++ + EPSGA+ LA KQ +A H + + Sbjct: 261 CQRHVDAMLRVDTDAICAAIRDVFQETRSVPEPSGALALAG-----LKQYAATHQLDDAT 315 Query: 318 IGIIVSGGNVD 328 + IVSG N++ Sbjct: 316 LVAIVSGANLN 326 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: 329 Number of extensions: 17 Number of successful extensions: 4 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: 523 Length adjustment: 32 Effective length of query: 307 Effective length of database: 491 Effective search space: 150737 Effective search space used: 150737 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