Align serine racemase (EC 5.1.1.18) (characterized)
to candidate 17824 b3772 threonine dehydratase (NCBI)
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Keio:17824 Length = 514 Score = 184 bits (466), Expect = 5e-51 Identities = 100/292 (34%), Positives = 165/292 (56%), Gaps = 2/292 (0%) Query: 24 ANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVLTFSSG 83 A TP+ ++ + K E+ Q + +FK RGA ++ L E Q+ GV+T S+G Sbjct: 29 AQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAG 88 Query: 84 NHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKEISER 143 NHAQ +A S+ LG+ A I+MP + KV A +G+GG+V+++ D+ + A E+S++ Sbjct: 89 NHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQ 148 Query: 144 EGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGGLLSGSALAARHFAPNCE 203 +G T +PP+DHP V+AGQGT A EL ++ LD +FV +GGGGL +G A+ + P + Sbjct: 149 QGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIK 208 Query: 204 VYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDILTVSDE 263 V VE E + + G V + A+G + +G+ TF + +E +DDI+TV + Sbjct: 209 VIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSD 268 Query: 264 ELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNVD 313 + +K ++ V EP+G L+ A + ++ +R+ I+SG NV+ Sbjct: 269 AICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVN 320 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: 342 Number of extensions: 12 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: 514 Length adjustment: 31 Effective length of query: 292 Effective length of database: 483 Effective search space: 141036 Effective search space used: 141036 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