Align serine racemase (EC 5.1.1.18) (characterized)
to candidate AZOBR_RS06795 AZOBR_RS06795 serine/threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__azobra:AZOBR_RS06795 Length = 331 Score = 231 bits (590), Expect = 1e-65 Identities = 121/319 (37%), Positives = 185/319 (57%), Gaps = 7/319 (2%) Query: 10 YDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLN 69 + D+ A+ R+ FA +TP+L ++ +N+ V K E Q+ G+FKFRGA N LSQL Sbjct: 11 HQDIVEAAARLDGFAVRTPLLENALLNERVGGRVLLKPEVLQRSGSFKFRGAFNRLSQLT 70 Query: 70 EAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRY 129 +R+ GV+ +SSGNHAQ +A +A +LG+PA I+MP DAP K+A T+GYG +V++YDR+ Sbjct: 71 PEERRGGVVAWSSGNHAQGVAAAAALLGMPAVIVMPSDAPALKIANTRGYGAEVVLYDRW 130 Query: 130 KDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVG-----PLDALFVCLGG 184 + RE +A I+E G +PPYDHP ++AGQGT E+ + P D + C G Sbjct: 131 TESREAIATAIAEERGAATVPPYDHPQIMAGQGTVGLEIAAQAQAIGAVPDDVIAPC-SG 189 Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGS-IVHIDTPKTIADGAQTQHLG 243 GGL+SG A A RH P+ ++ EP +D +S G + + ++I D T G Sbjct: 190 GGLMSGVATAVRHSFPDARLWAAEPAGFDDVARSLAAGERVENAAGQRSICDALLTPTPG 249 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303 TF ++K+ + L V+D E+ + + +K+VVEP G + AA K + + Sbjct: 250 ALTFPVMKDLLSGSLAVTDAEVKAAMAYAFTVLKLVVEPGGAVGLAAVLTGKLPAAGRTV 309 Query: 304 GIIISGGNVDIERYAHFLS 322 +++SGGNVD + L+ Sbjct: 310 AVVLSGGNVDAATFTDALA 328 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: 242 Number of extensions: 7 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: 331 Length adjustment: 28 Effective length of query: 295 Effective length of database: 303 Effective search space: 89385 Effective search space used: 89385 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 17 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