Align serine racemase (EC 5.1.1.18) (characterized)
to candidate GFF2535 PS417_12925 serine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__WCS417:GFF2535 Length = 321 Score = 430 bits (1105), Expect = e-125 Identities = 206/316 (65%), Positives = 256/316 (81%) Query: 8 PTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQ 67 PTY DV A++R++ A+ TPV TS T++ A+VF KCE+ Q+ G+FKFRGA NALSQ Sbjct: 4 PTYQDVIDAAQRLEGVAHATPVFTSRTLDALTGAQVFIKCEHLQRAGSFKFRGAFNALSQ 63 Query: 68 LNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYD 127 N QRKAGV+ FSSGNHAQ IAL+A++LGIPA I+MP DAP AKVAAT+ YG V++YD Sbjct: 64 FNPQQRKAGVVAFSSGNHAQGIALAAQLLGIPATIVMPTDAPAAKVAATREYGASVVLYD 123 Query: 128 RYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGGL 187 R+ +DRE++ + ++ +GLT+IPPYDHPH+LAGQGTAAKEL E GPLDALFV LGGGG+ Sbjct: 124 RFTEDREQIGRNLATEQGLTLIPPYDHPHILAGQGTAAKELLESTGPLDALFVGLGGGGM 183 Query: 188 LSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTF 247 LSG+AL+ R +P+C +YGVEPEAGNDGQ+SFR GSIVHIDTPKTIADGAQTQHLGNYTF Sbjct: 184 LSGTALSTRALSPDCLLYGVEPEAGNDGQRSFRSGSIVHIDTPKTIADGAQTQHLGNYTF 243 Query: 248 SIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGIII 307 II++ V+DILTVSD EL+ +KF+ RMK+VVEPTGCL AA + K +R+GII+ Sbjct: 244 PIIRDNVNDILTVSDAELVAAMKFFMQRMKMVVEPTGCLGLAALLNEAGRFKGQRVGIIV 303 Query: 308 SGGNVDIERYAHFLSQ 323 +GGNVDIE+YA LS+ Sbjct: 304 TGGNVDIEKYAALLSE 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: 337 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: 321 Length adjustment: 28 Effective length of query: 295 Effective length of database: 293 Effective search space: 86435 Effective search space used: 86435 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