Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_051402369.1 N177_RS12980 threonine/serine dehydratase
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_000496075.1:WP_051402369.1 Length = 340 Score = 218 bits (554), Expect = 2e-61 Identities = 128/309 (41%), Positives = 189/309 (61%), Gaps = 11/309 (3%) Query: 15 IKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQ 74 ++ A +R+ RTP++ S L+ +GR + K E LQ+ G+FKFRGA NA+ SLDA+ Sbjct: 25 VRRASERLSGEAVRTPLVRSAILDERAGRPVLLKAEVLQRTGSFKFRGAYNAIASLDADA 84 Query: 75 AAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSS 134 AKGVV SSGNHA ++ AA++ G+ A IV+P AP KV R G V+ + S Sbjct: 85 RAKGVVACSSGNHAQGVAEAARLFGVRATIVMPADAPALKVARTKRSGAHVVTYDRVNES 144 Query: 135 REEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEID----AIVVPISGGGLI 190 REEIA +++ ETG+ + PY+D R+ISGQGT+ +E+ EQ + + I+VP SGGGL Sbjct: 145 REEIALRIVAETGADFVPPYDDRRVISGQGTVGIEIAEQAEALGLDPARILVPCSGGGLS 204 Query: 191 SGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAG-KIITLPVTNTIADGLRASL-GDLTW 248 +G+ALAA+++ P R+ EP+ DD A+S +G + + +I D L A G++T+ Sbjct: 205 AGIALAAEALMPWARVTTVEPEAFDDHARSFRSGEREGNTARSGSICDALLADRPGEITF 264 Query: 249 PVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKN 308 V R V + + + E+ AM+ +E LK+ VEP GA+GLAAVL+ P + Sbjct: 265 AVNRPRVPSGLAVSDDEVRTAMRFAFEELKLVVEPGGAVGLAAVLAGRLDEGP-----QP 319 Query: 309 IGIVLSGGN 317 + +VLSGGN Sbjct: 320 VVVVLSGGN 328 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: 285 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: 331 Length of database: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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: 49 (23.5 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