Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_011319503.1 AVA_RS13915 threo-3-hydroxy-L-aspartate ammonia-lyase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000204075.1:WP_011319503.1 Length = 329 Score = 341 bits (874), Expect = 2e-98 Identities = 171/314 (54%), Positives = 225/314 (71%) Query: 9 TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68 T DV +A +R+ A++TPVLTS+TVN +VFFKCENFQ+ GAFKFRGA NAL+QL Sbjct: 8 TITDVQAAQQRLAGIAHRTPVLTSTTVNDRTHNQVFFKCENFQRTGAFKFRGAYNALAQL 67 Query: 69 NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128 + Q+ GVLTFSSGNH QAIAL+ K+L IP I+MP DAP K ATK YG +VI+Y+R Sbjct: 68 SPTQKHKGVLTFSSGNHGQAIALAGKLLNIPTTIVMPDDAPVIKQTATKSYGAEVILYNR 127 Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGGLL 188 + +RE++A+ ++ GLT+IPPYDHPHV+AGQGTAA EL +E+G LD L VC GGGGL+ Sbjct: 128 QETNREELAQNLASDRGLTLIPPYDHPHVIAGQGTAALELVQEIGELDLLLVCCGGGGLI 187 Query: 189 SGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFS 248 SG A+AA+ PN V GVEP +D +SF ++ + P TIADGA+T LG TF Sbjct: 188 SGCAIAAKALLPNLRVIGVEPTLADDATRSFYTKTLQTVTNPHTIADGARTPSLGQMTFP 247 Query: 249 IIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGIIIS 308 ++ + VDD++TVS+E +I + F R+KIVVEPTG L+ AA K + KRIG+IIS Sbjct: 248 LVLQYVDDMVTVSEEAIIRTMFFLWERLKIVVEPTGVLAAAALLENVVKAQGKRIGVIIS 307 Query: 309 GGNVDIERYAHFLS 322 GGNVD+ + A +++ Sbjct: 308 GGNVDLTKVASYVN 321 Lambda K H 0.318 0.135 0.384 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: 272 Number of extensions: 5 Number of successful extensions: 1 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: 323 Length of database: 329 Length adjustment: 28 Effective length of query: 295 Effective length of database: 301 Effective search space: 88795 Effective search space used: 88795 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 (21.7 bits) S2: 48 (23.1 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