Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_066603969.1 V473_RS11265 threonine/serine dehydratase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_001046645.1:WP_066603969.1 Length = 330 Score = 209 bits (531), Expect = 1e-58 Identities = 116/315 (36%), Positives = 176/315 (55%), Gaps = 5/315 (1%) Query: 9 TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68 T D+ A+ I A +TP+L + +N V K E Q G+FKFRGA N L++L Sbjct: 8 TIHDIIDAARIIAPAAVRTPLLENHALNDRLGRRVLIKFEGAQHTGSFKFRGAYNRLARL 67 Query: 69 NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128 + QR AGV+ +SSGNHAQ +A +A++L +PA I+MP DAP K+A + G +++ YDR Sbjct: 68 DAQQRAAGVVAWSSGNHAQGVAAAAQLLALPATIVMPSDAPAIKLANNRALGAEIVTYDR 127 Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDA----LFVCLGG 184 + + RE++A ++ G T++P +D P V+AGQGTA E+ ++ A + VC GG Sbjct: 128 HSESREEIATALAHSRGATLVPSFDDPFVIAGQGTAGLEILDQAAEAGAIIGQILVCCGG 187 Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHI-DTPKTIADGAQTQHLG 243 GGL +G A A + AP +Y VEP +D +S G +I ++I D G Sbjct: 188 GGLTAGIATAVKARAPEIALYAVEPAGFDDTARSLASGVRENIAPDARSICDALMAPSPG 247 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303 TF I + + L VSD+++ D ++F + +K+VVEP G ++ AA Sbjct: 248 AMTFPINQALLSGGLVVSDDQVRDAMRFAFSTLKLVVEPGGAVALAAVLNGLAPPCGDAS 307 Query: 304 GIIISGGNVDIERYA 318 +++SG NVD YA Sbjct: 308 VVVLSGSNVDPAAYA 322 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: 219 Number of extensions: 6 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: 323 Length of database: 330 Length adjustment: 28 Effective length of query: 295 Effective length of database: 302 Effective search space: 89090 Effective search space used: 89090 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