Align serine racemase (EC 5.1.1.18) (characterized)
to candidate PP_5149 PP_5149 threonine deaminase
Query= BRENDA::Q2PGG3 (331 letters) >FitnessBrowser__Putida:PP_5149 Length = 504 Score = 193 bits (491), Expect = 7e-54 Identities = 113/289 (39%), Positives = 167/289 (57%), Gaps = 7/289 (2%) Query: 6 EKYAADILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACN 65 E+Y IL+ R+ TP+ ++ L+ G + K E LQ +FK RGA N Sbjct: 3 EQYVKKILT-----SRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYN 57 Query: 66 AVLSLDAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKV 125 + L E+ A+GVVT S+GNHA L+LAA+ GI A IV+PK P+ KV+ V GGKV Sbjct: 58 KLAQLSPEELARGVVTASAGNHAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKV 117 Query: 126 IWSEATMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQ-EIDAIVVPI 184 + + + K++ E G V +HPY+D I+GQGT+A+E+L Q +DAI VP+ Sbjct: 118 VLHGDSFPEALAYSLKLVDEKGFVYVHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPV 177 Query: 185 SGGGLISGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLR-ASL 243 GGGLI+G+A K ++P I+II EP ++ + AG+ + LP ADG+ A + Sbjct: 178 GGGGLIAGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQI 237 Query: 244 GDLTWPVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAV 292 G T+ + R VD+VVT+ EI A+K Y+ + EP+GA+G+A + Sbjct: 238 GQHTFDICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGI 286 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: 350 Number of extensions: 13 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: 331 Length of database: 504 Length adjustment: 31 Effective length of query: 300 Effective length of database: 473 Effective search space: 141900 Effective search space used: 141900 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