Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_085985190.1 MICLODRAFT_RS33510 threonine ammonia-lyase, biosynthetic
Query= BRENDA::O59791 (323 letters) >NCBI__GCF_000262405.1:WP_085985190.1 Length = 519 Score = 179 bits (453), Expect = 2e-49 Identities = 99/280 (35%), Positives = 156/280 (55%), Gaps = 3/280 (1%) Query: 43 VFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKI 102 V K E+ Q + +FK RGA ++ L + GV+ S+GNHAQ +A++AK LG A I Sbjct: 44 VRLKREDLQPVFSFKLRGAYARMAGLPREALERGVICASAGNHAQGVAVAAKKLGAKATI 103 Query: 103 IMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQG 162 +MP P K+ A KG GG+VI++ D+ A+++ +GLT I PYD P V+AGQG Sbjct: 104 VMPRTTPAIKIQAVKGQGGRVILHGESFDEAYSHAQQLEAEKGLTFIHPYDDPDVIAGQG 163 Query: 163 TAAKELF-EEVGPLDALFVCLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRK 221 T E+ + PL+A+FV +GGGGL +G A+ + P +V GVEPE + Sbjct: 164 TVGMEILRQHPDPLEAIFVPIGGGGLAAGVAVYTKFLRPEVKVIGVEPEDAASMAAALAA 223 Query: 222 GSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVE 281 G V ++ ADG + G TF + +E +D+++TVS +E+ +K + + E Sbjct: 224 GDRVILNQVGLFADGVAVRQAGEETFRLCRELLDEVITVSTDEICAAVKDIFEDTRAIAE 283 Query: 282 PTGCLSFAAARAMKEKLKNKRIGIII--SGGNVDIERYAH 319 P+G +S A + E+ ++ G++ SG N++ +R H Sbjct: 284 PSGAVSLAGLKKYVEREGARQQGLVAVNSGANMNFDRLRH 323 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: 345 Number of extensions: 12 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: 519 Length adjustment: 31 Effective length of query: 292 Effective length of database: 488 Effective search space: 142496 Effective search space used: 142496 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