Align Lysine racemase; Lys racemase; Ornithine racemase; EC 5.1.1.5; EC 5.1.1.12 (characterized)
to candidate WP_158090989.1 MGEO_RS07780 alanine/ornithine racemase family PLP-dependent enzyme
Query= SwissProt::Q9X1T3 (354 letters) >NCBI__GCF_002115805.1:WP_158090989.1 Length = 379 Score = 207 bits (528), Expect = 3e-58 Identities = 115/349 (32%), Positives = 191/349 (54%), Gaps = 3/349 (0%) Query: 4 PRLLINLKEIEENARKVVEMASRRGIEIVGVTKVTLGDPRFAETLRKAGIGILGESRIRN 63 PR+ + +++N + ++ + GI + GVTK G+P A + GI L ++R+ N Sbjct: 10 PRVEFDTDALQQNFAHLAKLCAAHGIAVSGVTKAIGGNPDIARLMLDNGIRTLADARLDN 69 Query: 64 VLRMKKAGIEGPFMLLRLPMMSELVEDVKHFDYIMVSDPDVAKKVDELSREMKRNVKIIY 123 + R++ GI+ P MLLR P M E+ E + D ++S+ + + + E+ + +++ Sbjct: 70 IARLRAGGIDVPVMLLRAPAMVEVAEAARLADIFLLSEIETIRALATAKAELGKCCQVVL 129 Query: 124 MIDVGDLREGVWFEKAVE---EIAQCRGANIVGIGTNFGCYGGIIPTREKFEILLDIKEK 180 M+D+GDLREGV E + ANI+GIGTN C G++P + L+ + + Sbjct: 130 MVDLGDLREGVPPEDLPSLGRAVMATENANIIGIGTNLACNLGVLPDQSNMAELVALANQ 189 Query: 181 LEKNHGFNIEIVSGGNTPALYALENGEIPEGINQLRIGEAIVLGRDITNNRVIDWLSQNT 240 LE G + VS GN+ A+ + N +P IN LR+GE+++LGR+ + +S + Sbjct: 190 LEATIGHPLRYVSAGNSSAISLMLNQGLPSKINHLRLGESLLLGRETAYGHPLARMSGDC 249 Query: 241 FLIEAEVIEVKEKPSVPLGKRGLDVFGRKVDFVDRGIRKRAICALGEQDIDSRGLIPVDK 300 F + A++IE K K P RG + FG++VD R+ + +G D + GL P+ Sbjct: 250 FDLVAQIIEHKLKAPRPYAARGRNAFGQQVDVELTEPRRLGVLNVGAVDCEIGGLCPLIN 309 Query: 301 GVEVLHASSDHIVLDVTDFGDVKVGDVFRFRMTYSCLLKAMTSPFVEKV 349 GV ++ SSDH+++D T + VGD RFR+ Y L AMTSP++ +V Sbjct: 310 GVSIVGYSSDHLIVDTTSSTSLAVGDEIRFRVDYHALATAMTSPYLAQV 358 Lambda K H 0.321 0.142 0.407 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: 302 Number of extensions: 7 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: 354 Length of database: 379 Length adjustment: 30 Effective length of query: 324 Effective length of database: 349 Effective search space: 113076 Effective search space used: 113076 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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