Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_068002199.1 PsAD2_RS03350 threonine/serine dehydratase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_001623255.1:WP_068002199.1 Length = 339 Score = 225 bits (574), Expect = 1e-63 Identities = 126/320 (39%), Positives = 181/320 (56%), Gaps = 5/320 (1%) Query: 9 TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68 T ++ A R++ +++ TP+L +++ VF K EN Q+ G+FKFRGA N LS + Sbjct: 12 TVSEIEKARARLQGYSSMTPLLNYPVLDERVNGRVFIKAENLQRTGSFKFRGAFNRLSLI 71 Query: 69 NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128 + QR GV+ SSGNHAQ +A SAKILG PA I+MP DAPE K+ TK G +VI+Y R Sbjct: 72 PQGQRAGGVVACSSGNHAQGVAASAKILGFPAVIVMPKDAPELKIQRTKALGAEVILYCR 131 Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPL----DALFVCLGG 184 + +DRE +A I E G T I P++ V+ GQGT+ E+ E+ L D L C GG Sbjct: 132 HSEDREAIAHAICEERGATFIHPFNDSGVIVGQGTSGLEIVEQCEALGVSPDVLISCTGG 191 Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIV-HIDTPKTIADGAQTQHLG 243 GGL SG ALA P+C++Y EP +D +S G V + ++ D T G Sbjct: 192 GGLTSGIALALEKSLPDCQIYTAEPAGFDDYARSLESGERVRNAALSGSVCDAIMTDTPG 251 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303 +F+I+K + L+VSDE+ + + + +K+VVEP ++ A+ + + L K Sbjct: 252 EKSFAILKRRQAKGLSVSDEQAMHAVAYAYFELKLVVEPGAAVALASLLSGQIDLDGKTA 311 Query: 304 GIIISGGNVDIERYAHFLSQ 323 I ISGGNVD + L Q Sbjct: 312 VITISGGNVDPSVFEAALKQ 331 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: 238 Number of extensions: 12 Number of successful extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 295 Effective length of database: 311 Effective search space: 91745 Effective search space used: 91745 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: 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