Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_044050245.1 RCA23_RS10315 threonine/serine dehydratase
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000738435.1:WP_044050245.1 Length = 325 Score = 212 bits (540), Expect = 9e-60 Identities = 123/314 (39%), Positives = 184/314 (58%), Gaps = 5/314 (1%) Query: 13 VASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQ 72 + +A++R++ A +TP+L S+ V++ V+ K E Q G+FKFRG +A+S L Sbjct: 6 IRAAAQRLEGQARRTPLLNSAFVDEIAGRRVWVKAEALQHTGSFKFRGGWSAVSALAAEV 65 Query: 73 RKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDD 132 R AGV+ +SSGNHAQ +AL+A++ G+PA I+MP DAP KV T+ G +VI+YDR +D Sbjct: 66 RSAGVIAYSSGNHAQGVALAARLHGVPAVIVMPKDAPRLKVENTRALGAEVILYDRDHED 125 Query: 133 REKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKEL---FEEVGPLDA-LFVCLGGGGLL 188 RE + ++E GL++I PYD P V+AGQGT E+ EVG A + VC GGGGL Sbjct: 126 REAIGAALAEARGLSLIKPYDAPEVIAGQGTCGLEIAAQAAEVGIAKADVLVCCGGGGLT 185 Query: 189 SGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKG-SIVHIDTPKTIADGAQTQHLGNYTF 247 SG ALA AP+ V VEP +D +S + G + + +I D T+ G TF Sbjct: 186 SGVALALEQEAPDMRVRPVEPVDFDDVTRSLQSGRRESNTRSGGSICDAIVTRSPGEMTF 245 Query: 248 SIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGIII 307 ++ E + V +E+ + + +R K+V+EP G ++ AAA E+L + + I Sbjct: 246 PLMHELCGPGIVVPEEDCLRAISVAFSRFKLVLEPGGAIALAAALYHGEQLSGEHVICIA 305 Query: 308 SGGNVDIERYAHFL 321 SGGN+D + + L Sbjct: 306 SGGNIDAQMFTRAL 319 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: 237 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: 325 Length adjustment: 28 Effective length of query: 295 Effective length of database: 297 Effective search space: 87615 Effective search space used: 87615 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