Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_009491092.1 MICLODRAFT_RS10110 threonine ammonia-lyase
Query= BRENDA::Q2PGG3 (331 letters) >NCBI__GCF_000262405.1:WP_009491092.1 Length = 423 Score = 207 bits (526), Expect = 5e-58 Identities = 122/321 (38%), Positives = 189/321 (58%), Gaps = 10/321 (3%) Query: 1 MEANREKYAADILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKF 60 +E + YA I +K A + I+ + RTP++ + L+ ++G ++F K E +Q G+FK Sbjct: 7 LEDDVADYAITIEDVKRAAETIQGQVLRTPLVPAPRLSQLTGSTVFVKHENMQPTGSFKE 66 Query: 61 RGACNAVLSLDAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIR 120 RGA + SL + GV+ S+GNHA A++ A+ GIPA IV+P G P K +N Sbjct: 67 RGATTKLESLTEAERKHGVIAMSAGNHAQAVAYHARRLGIPATIVMPVGTPLVKAENTRS 126 Query: 121 YGGKVIWSEATMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAI 180 YG +VI T+ A ++ G V +HPY+D ++++GQGTIALE+L ++D I Sbjct: 127 YGARVILEGETLYESAARAREIADAEGLVFVHPYDDPKVMAGQGTIALEMLADAPDLDQI 186 Query: 181 VVPISGGGLISGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTN-TIADGL 239 VVPI GGGLISG+A+AAK++KPS II E + ++ + G+ P+ T+A+G+ Sbjct: 187 VVPIGGGGLISGIAIAAKALKPSTEIIGVE-AALYPSFRNAILGE--NRPIGGATLAEGI 243 Query: 240 RA-SLGDLTWPVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFR 298 ++G L P+VRDLV +++ +EE I A+ + + E +GA GLAA+L+ Sbjct: 244 AVKTVGQLPLPIVRDLVPNIIAVEEPLIERAVNAYATLQRTMAEGAGAAGLAAMLA---- 299 Query: 299 NNPSCRDCKNIGIVLSGGNVD 319 P K +G+VL GGN+D Sbjct: 300 -QPERFQGKRVGLVLCGGNID 319 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: 307 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: 423 Length adjustment: 30 Effective length of query: 301 Effective length of database: 393 Effective search space: 118293 Effective search space used: 118293 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