Align serine racemase (EC 5.1.1.18) (characterized)
to candidate HSERO_RS19510 HSERO_RS19510 threonine dehydratase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__HerbieS:HSERO_RS19510 Length = 508 Score = 185 bits (469), Expect = 2e-51 Identities = 101/306 (33%), Positives = 171/306 (55%), Gaps = 8/306 (2%) Query: 19 RIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVL 78 R+ A +TP+ ++T+++ ++FK E+ Q + +FK RGA N ++ L AQ K GV+ Sbjct: 13 RVYDVAQETPLELANTLSQRIDNRIYFKREDMQSVFSFKLRGAYNKMAHLTPAQLKRGVI 72 Query: 79 TFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAK 138 S+GNHAQ +ALSA LG A I+MP P+ K+ A K GG+V+++ D + A Sbjct: 73 CASAGNHAQGVALSAARLGCRAVIVMPTTTPQVKIDAVKARGGEVVLFGDSFTDAYEHAL 132 Query: 139 EISEREGLTIIPPYDHPHVLAGQGTAAKELF-EEVGPLDALFVCLGGGGLLSGSALAARH 197 + +++ LT + P+D P+V+AGQGT E+ + P+ A+FV +GGGGL++G A + Sbjct: 133 TLEKKQKLTFVHPFDDPYVIAGQGTVGMEILRQHPDPIHAIFVAIGGGGLIAGVASYVKA 192 Query: 198 FAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDI 257 P+ ++ GV+ + +S + G V + +DG + +G TF I KE VD++ Sbjct: 193 VRPDIKIIGVQTTDSDAMARSLKAGRRVALPDVGLFSDGTAVKLVGEETFRIAKELVDEV 252 Query: 258 LTVSDEELIDCLKFYAARMKIVVEPTGCLSFAA-------ARAMKEKLKNKRIGIIISGG 310 + V + + +K + +VEP G L+ A A+A K+ +K + + I G Sbjct: 253 IIVDTDAVCTAIKDIFQDTRSIVEPAGALAVAGAKAYVERAKASKKPIKGESLITIACGA 312 Query: 311 NVDIER 316 N++ +R Sbjct: 313 NMNFDR 318 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: 349 Number of extensions: 10 Number of successful extensions: 2 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: 508 Length adjustment: 31 Effective length of query: 292 Effective length of database: 477 Effective search space: 139284 Effective search space used: 139284 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: 50 (23.9 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