Align Lysine racemase; Lys racemase; Ornithine racemase; EC 5.1.1.5; EC 5.1.1.12 (characterized)
to candidate 3608907 Dshi_2298 alanine racemase domain protein (RefSeq)
Query= SwissProt::Q9X1T3 (354 letters) >FitnessBrowser__Dino:3608907 Length = 373 Score = 165 bits (418), Expect = 2e-45 Identities = 127/355 (35%), Positives = 187/355 (52%), Gaps = 15/355 (4%) Query: 1 MVYPRLLINLKEIEENARKVVEMASRRGIEIVGVTKVTLGDPRFAETLRKAGIGILGESR 60 M PRL ++L +I NA+ + + RG+ I VTK G+P A + + G L E+R Sbjct: 1 MKNPRLEVDLCKIRHNAQTLAGRLTPRGLGITAVTKAVCGNPAIARAMLEGGAVGLAEAR 60 Query: 61 IRNVLRMKKAGIEGPFMLLRLPMMSELVEDVKHFDYIMVSDPDVAKKVDELSREMKRNVK 120 +RNV R+++AG+ L+R PM+SE E V+ + SD V + S + Sbjct: 61 LRNVRRLREAGLTCAVTLIRTPMLSEAAEVVRLCETSFNSDLRVISALSAESCPRRAAHG 120 Query: 121 IIYMIDVGDLREGVWFEKAVEEIAQCR---GANIVGIGTNFGCYGGIIPTREKFEILLDI 177 II M+++GDLREG+ E+ + R G + GIG NF C+GG P L DI Sbjct: 121 IILMVEMGDLREGILPEELGALALRVRALPGVVLQGIGANFACFGGQAPEPAIMMALSDI 180 Query: 178 KEKLEKNHGFNIEIVSGGNTPAL-YALENGEIPEG-INQLRIGEAIVLGRDITNNRVIDW 235 + E+ G ++ VSGGN+ L +A+ G P G I LR+GEAI+LG + + I Sbjct: 181 VVETERTCGVILQTVSGGNSANLPWAM--GATPTGRITDLRLGEAILLGVEPVSGDRIAG 238 Query: 236 LSQNTFLIEAEVIEVKEKPSVPLGKRGLDVFGRKVDFVDRGIR-KRAICALGEQDIDSRG 294 L + + AEVIE K S+P GR++ R R R I ALG QD D +G Sbjct: 239 LHTDAITLVAEVIEAGFK-SLPSRAAKATASGRRI----RPSRTTRLILALGVQDTDVQG 293 Query: 295 LIPVDKGVEVLHASSDHIVLDVTDFGDVKVGDVFRFRMTYSCLLKAMTSPFVEKV 349 L+ + G + A+SDH+V+ VT + G RF++ YS L++AM +P +E V Sbjct: 294 LV-MPVGTTFVGATSDHLVV-VTQNALPRPGGEMRFQLNYSALMRAMAAPDIETV 346 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: 295 Number of extensions: 11 Number of successful extensions: 5 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: 373 Length adjustment: 29 Effective length of query: 325 Effective length of database: 344 Effective search space: 111800 Effective search space used: 111800 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 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