Align Ornithine racemase; OR; EC 5.1.1.12 (characterized)
to candidate Echvi_2799 Echvi_2799 Predicted amino acid racemase
Query= SwissProt::C1FW08 (353 letters) >FitnessBrowser__Cola:Echvi_2799 Length = 356 Score = 229 bits (584), Expect = 8e-65 Identities = 134/347 (38%), Positives = 202/347 (58%), Gaps = 6/347 (1%) Query: 12 LRDNATFIKNLCEKGGCKTALVVKSMCANHDIVKELDSVEVDYFADSRIQNLKKLKDLKT 71 L+ N F+K ++ G V K +C N +KEL + VD DSRI NL K+K++ + Sbjct: 11 LQKNYQFLKEKFKEHGVAWGAVSKMLCGNEIYIKELIDLGVDEIHDSRISNLVKVKEINS 70 Query: 72 --KKMLLRIPMLCEVEDVVKYADISMNSELDTLKALNKAAKTLNKVHSVIIMVDLGDLRE 129 K + ++ P + DVV YAD+S+NSEL T++ +++ A +K H +IIMV+ GDLRE Sbjct: 71 NIKTVYIKPPSKRNLADVVTYADVSLNSELTTIRWISEEAVRQDKRHQIIIMVETGDLRE 130 Query: 130 GYFEAEDLKENIKEIIKLENIEIKGIGVNLTCYGAVIPKNDNLSRLCDIADELRTEFNLE 189 G EDL + +I +L N+E+ G+G NL C V+P D L +L + +FN E Sbjct: 131 GVM-GEDLVDFYAKIFRLPNVEVIGLGTNLNCLNGVMPSTDKLVQLSLYKQIIELKFNKE 189 Query: 190 LPIVSGGNSSSIYLIDKGELPEGITNLRVGESMLLGRETAYGEDIIGMNNDVFELKCQIV 249 +P+VS G S +I L+ +LP+G+ + RVGE++ G I GMN+ VFEL +I+ Sbjct: 190 IPLVSAGTSVTIPLMLNHQLPKGVNHFRVGETLYFGANLFDESTIPGMNDAVFELCTEII 249 Query: 250 ELKEKPSLPIGEIGVDAFGNKPYYEDKGIRK---RAILAIGQQDTDISSLMPIDDKLEIL 306 E++EKP LP G + + G+ ++ + R IL IG D D L+ D+ E+L Sbjct: 250 EMQEKPLLPTGNLAANPQGDIKEIDESLYGQSSFRGILDIGLLDVDPKYLIYDKDEFEVL 309 Query: 307 GASSDHLIVDVSDSNTSYKVGDIITFRMGYGALLKGFTSEYIEKELL 353 GASSD LI+D+ + +YKVGD+I F++ Y L S YIEK ++ Sbjct: 310 GASSDMLILDLGKNPKNYKVGDLIRFKLKYMGALAILNSYYIEKRVI 356 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: 346 Number of extensions: 22 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: 356 Length adjustment: 29 Effective length of query: 324 Effective length of database: 327 Effective search space: 105948 Effective search space used: 105948 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 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