Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate N515DRAFT_0537 N515DRAFT_0537 threonine dehydratase
Query= BRENDA::Q54HH2 (324 letters) >FitnessBrowser__Dyella79:N515DRAFT_0537 Length = 315 Score = 286 bits (732), Expect = 5e-82 Identities = 149/311 (47%), Positives = 211/311 (67%), Gaps = 4/311 (1%) Query: 9 LKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSLD 68 L I++A RI Y TPVL ++ ++ LAG +L+FKCENLQ+ G+FK RGACNA++SLD Sbjct: 7 LDQIRDAAARIAPYAAVTPVLRSARLDALAGAQLHFKCENLQRGGAFKFRGACNAVWSLD 66 Query: 69 EEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCKAT 128 + + ++GVVTHSSGNHG AL+ A+ R + +VVVPE A KL AI GA + +C T Sbjct: 67 DAQAARGVVTHSSGNHGNALAMAAATRGIAAHVVVPEGAVRAKLEAIEQAGAVLHRCAPT 126 Query: 129 LEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENLDAIITPVGGGGLLS 188 ARE+ T +L Q +L+HP+ + +V+AGQGT LELM QVE LDA+ITPVGGGGL + Sbjct: 127 TAAREAMTAELQRQTGAELVHPYADARVMAGQGTLVLELMRQVEGLDALITPVGGGGLAA 186 Query: 189 GTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTVGSLTFP 248 G I A L P + ++ AEP GADD RSL G + P + +T+ DGL T +G+ F Sbjct: 187 GCAIAAHGLKPELAMYGAEPTGADDAARSLAQG--ARVEPFQADTLCDGLRTLIGAPNFD 244 Query: 249 IIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKVGII 308 ++ + VI V+++E AMKL+W +K+++E SSAT LAA+LKQ + ++VG++ Sbjct: 245 ALRTHRTQVITVSDEETIAAMKLLWRELKLVVEVSSATVLAAVLKQ--AEHFAGRRVGLV 302 Query: 309 ISGGNVDLSSI 319 ++GGNVDL ++ Sbjct: 303 LTGGNVDLDAL 313 Lambda K H 0.315 0.132 0.374 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: 267 Number of extensions: 12 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: 324 Length of database: 315 Length adjustment: 28 Effective length of query: 296 Effective length of database: 287 Effective search space: 84952 Effective search space used: 84952 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 (21.5 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