Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_090446659.1 BLS63_RS16565 threonine ammonia-lyase, biosynthetic
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_900100495.1:WP_090446659.1 Length = 504 Score = 199 bits (505), Expect = 2e-55 Identities = 118/320 (36%), Positives = 180/320 (56%), Gaps = 10/320 (3%) Query: 6 EKYAADILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACN 65 E+Y IL+ R+ TP+ ++ L+ G + K E LQ +FK RGA N Sbjct: 3 EQYVKKILT-----SRVYDVAVETPLQAAQQLSERLGNQILLKREDLQPVYSFKIRGAYN 57 Query: 66 AVLSLDAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKV 125 + L AE+ A+GVVT S+GNHA ++LAAK+ G+ A IV+PK P+ KV V GGKV Sbjct: 58 KLAQLTAEEQARGVVTASAGNHAQGVALAAKVLGVKATIVMPKTTPEIKVQGVRSRGGKV 117 Query: 126 IWSEATMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQ-EIDAIVVPI 184 + + + K+++E G + +HPY+D I+GQGT+A+E+L Q ++DAI VP+ Sbjct: 118 VLHGDSFPEALAYSLKLVEEKGYIYVHPYDDPHTIAGQGTVAMEILRQHPGQLDAIFVPV 177 Query: 185 SGGGLISGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTNTIADGLR-ASL 243 GGGLI+G+A K ++P I++I EP ++ + AG+ + LP ADG+ A + Sbjct: 178 GGGGLIAGIAAYVKYLRPEIKVIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQV 237 Query: 244 GDLTWPVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSC 303 G+ T+ + R VD+V+T+ EI A+K Y+ + EP+GA+ +A + R S Sbjct: 238 GEYTFAICRHHVDEVITVSTDEICAAIKDIYDDTRSITEPAGALAVAGIKKYVEREGCSA 297 Query: 304 RDCKNIGIVLSGGNVDLGSL 323 R I SG NV+ L Sbjct: 298 RVLVGID---SGANVNFDRL 314 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: 362 Number of extensions: 15 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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 24 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