Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_004306745.1 C665_RS09355 threonine ammonia-lyase, biosynthetic
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000310185.1:WP_004306745.1 Length = 507 Score = 181 bits (458), Expect = 4e-50 Identities = 98/296 (33%), Positives = 166/296 (56%), Gaps = 3/296 (1%) Query: 24 ANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVLTFSSG 83 A +TP+ ++ ++ ++FK E+ Q + +FK RGA N ++ L+ K GV+ S+G Sbjct: 20 AVETPLDLATNLSARTHNRIYFKREDMQPVFSFKIRGAYNKMANLSPQALKRGVICASAG 79 Query: 84 NHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKEISER 143 NHAQ +ALSA LG+ A I+MP P+ K+ A K GG+V++ D A E+ + Sbjct: 80 NHAQGVALSAARLGVRAVIVMPSTTPQIKIDAVKARGGEVVLAGESYSDAYTHALELEKS 139 Query: 144 EGLTIIPPYDHPHVLAGQGTAAKELFE-EVGPLDALFVCLGGGGLLSGSALAARHFAPNC 202 E LT + P+D P V+AGQGT E+ P+ A+F C+GGGGL++G A + P Sbjct: 140 EKLTFVHPFDDPDVIAGQGTVGLEILRAHPKPIHAVFCCVGGGGLIAGVAAYIKRLRPET 199 Query: 203 EVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDILTVSD 262 ++ GVE + +S G + ++ ADGA + +G TF + ++ VD+++ V + Sbjct: 200 KIIGVEAVDADAMTRSLAAGKRIALEQVGIFADGAAVKEVGAETFRLCQQYVDEMIVVDN 259 Query: 263 EELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNKRIGIIISGGNVDIER 316 + + +K + ++EP G L+ A A+ A + KL++K + + SG N++ +R Sbjct: 260 DAICAAIKDVFEDTRSILEPAGALAVAGAKEYARRNKLRDKSLVAVASGANMNFDR 315 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: 335 Number of extensions: 8 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: 507 Length adjustment: 31 Effective length of query: 292 Effective length of database: 476 Effective search space: 138992 Effective search space used: 138992 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 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