Align Ornithine racemase; OR; EC 5.1.1.12 (characterized)
to candidate WP_158090989.1 MGEO_RS07780 alanine/ornithine racemase family PLP-dependent enzyme
Query= SwissProt::C1FW08 (353 letters) >NCBI__GCF_002115805.1:WP_158090989.1 Length = 379 Score = 225 bits (574), Expect = 1e-63 Identities = 137/348 (39%), Positives = 196/348 (56%), Gaps = 4/348 (1%) Query: 3 PKITIDINKLRDNATFIKNLCEKGGCKTALVVKSMCANHDIVKELDSVEVDYFADSRIQN 62 P++ D + L+ N + LC G + V K++ N DI + + + AD+R+ N Sbjct: 10 PRVEFDTDALQQNFAHLAKLCAAHGIAVSGVTKAIGGNPDIARLMLDNGIRTLADARLDN 69 Query: 63 LKKLK--DLKTKKMLLRIPMLCEVEDVVKYADISMNSELDTLKALNKAAKTLNKVHSVII 120 + +L+ + MLLR P + EV + + ADI + SE++T++AL A L K V++ Sbjct: 70 IARLRAGGIDVPVMLLRAPAMVEVAEAARLADIFLLSEIETIRALATAKAELGKCCQVVL 129 Query: 121 MVDLGDLREGYFEAEDLKENIKEIIKLENIEIKGIGVNLTCYGAVIPKNDNLSRLCDIAD 180 MVDLGDLREG EDL + ++ EN I GIG NL C V+P N++ L +A+ Sbjct: 130 MVDLGDLREGV-PPEDLPSLGRAVMATENANIIGIGTNLACNLGVLPDQSNMAELVALAN 188 Query: 181 ELRTEFNLELPIVSGGNSSSIYLIDKGELPEGITNLRVGESMLLGRETAYGEDIIGMNND 240 +L L VS GNSS+I L+ LP I +LR+GES+LLGRETAYG + M+ D Sbjct: 189 QLEATIGHPLRYVSAGNSSAISLMLNQGLPSKINHLRLGESLLLGRETAYGHPLARMSGD 248 Query: 241 VFELKCQIVELKEKPSLPIGEIGVDAFGNKPYYEDKGIRKRAILAIGQQDTDISSLMPID 300 F+L QI+E K K P G +AFG + E R+ +L +G D +I L P+ Sbjct: 249 CFDLVAQIIEHKLKAPRPYAARGRNAFGQQVDVELTEPRRLGVLNVGAVDCEIGGLCPLI 308 Query: 301 DKLEILGASSDHLIVDVSDSNTSYKVGDIITFRMGYGALLKGFTSEYI 348 + + I+G SSDHLIVD + S+TS VGD I FR+ Y AL TS Y+ Sbjct: 309 NGVSIVGYSSDHLIVDTT-SSTSLAVGDEIRFRVDYHALATAMTSPYL 355 Lambda K H 0.317 0.138 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: 262 Number of extensions: 12 Number of successful extensions: 4 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: 353 Length of database: 379 Length adjustment: 30 Effective length of query: 323 Effective length of database: 349 Effective search space: 112727 Effective search space used: 112727 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 (21.6 bits) S2: 49 (23.5 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