Align serine racemase (EC 5.1.1.18) (characterized)
to candidate N515DRAFT_0537 N515DRAFT_0537 threonine dehydratase
Query= BRENDA::Q2PGG3 (331 letters) >FitnessBrowser__Dyella79:N515DRAFT_0537 Length = 315 Score = 268 bits (686), Expect = 1e-76 Identities = 143/315 (45%), Positives = 209/315 (66%), Gaps = 9/315 (2%) Query: 11 DILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSL 70 D+ I++A RI PY TPVL S L++++G L FKCE LQ+GGAFKFRGACNAV SL Sbjct: 6 DLDQIRDAAARIAPYAAVTPVLRSARLDALAGAQLHFKCENLQRGGAFKFRGACNAVWSL 65 Query: 71 DAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEA 130 D QAA+GVVTHSSGNH AL++AA +GI A++VVP+GA + K++ + + G + Sbjct: 66 DDAQAARGVVTHSSGNHGNALAMAAATRGIAAHVVVPEGAVRAKLEAIEQAGAVLHRCAP 125 Query: 131 TMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAIVVPISGGGLI 190 T ++RE + +++ ++TG+ L+HPY D R+++GQGT+ LEL+ Q++ +DA++ P+ GGGL Sbjct: 126 TTAAREAMTAELQRQTGAELVHPYADARVMAGQGTLVLELMRQVEGLDALITPVGGGGLA 185 Query: 191 SGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLRASLGDLTWPV 250 +G A+AA +KP + + AEP GADDAA+S G + +T+ DGLR +G + Sbjct: 186 AGCAIAAHGLKPELAMYGAEPTGADDAARSLAQGARVEPFQADTLCDGLRTLIGAPNFDA 245 Query: 251 VRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNS--FRNNPSCRDCKN 308 +R V+T+ + E I AMK+ + LK+ VE S A LAAVL + F + Sbjct: 246 LRTHRTQVITVSDEETIAAMKLLWRELKLVVEVSSATVLAAVLKQAEHFAG-------RR 298 Query: 309 IGIVLSGGNVDLGSL 323 +G+VL+GGNVDL +L Sbjct: 299 VGLVLTGGNVDLDAL 313 Lambda K H 0.316 0.133 0.380 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: 287 Number of extensions: 10 Number of successful extensions: 2 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: 331 Length of database: 315 Length adjustment: 28 Effective length of query: 303 Effective length of database: 287 Effective search space: 86961 Effective search space used: 86961 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