Align proline racemase (EC 5.1.1.4) (characterized)
to candidate BPHYT_RS22640 BPHYT_RS22640 hydroxyproline-2-epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__BFirm:BPHYT_RS22640 Length = 318 Score = 188 bits (478), Expect = 1e-52 Identities = 117/331 (35%), Positives = 176/331 (53%), Gaps = 17/331 (5%) Query: 1 MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60 M +++ IDSHT GE TR+VV G P++ G ++ ++ + D R I+ EPRG + Sbjct: 1 MGIMKTLDIIDSHTGGEPTRLVVSGGPDLGGGTLAQRLDVFRTQFDDWRAGIVTEPRGSD 60 Query: 61 DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120 + G+++ +P P G+IF + GYL MCGHGTIG + + G + A H + E Sbjct: 61 VVVGALLCEPDDPTCAAGVIFFNNVGYLGMCGHGTIGLVVSLAHLGRIGAGR---HRI-E 116 Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180 P GI+ + DG V+ NVPA+ Y+ V+VD+PG G + DI +GG++F ++ Sbjct: 117 TPVGIVEATLN-DDG---SVAVRNVPAYRYRRSVQVDVPGHGVLTGDIGWGGNWFFLV-- 170 Query: 181 SQLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYK 240 + G +E G+LT + +RD + QH T A +D +E++ + + Sbjct: 171 ADHGRVLEASRIGELTTFSGAIRD----ALIAQHITGADGALIDHIELFGPGSRDGLDSR 226 Query: 241 NVVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVAD 300 + V+ DRSPCGTGTSAK+A L A G+L G + ESI+G++F+ D Sbjct: 227 SFVLCPGSAYDRSPCGTGTSAKVACLAADGKLAEGAVWRQESIIGSVFEASY---RHAGD 283 Query: 301 FNAVVPKITGSAYITGFNHFVIDEEDPLKHG 331 V+P ITG AYIT DE DP G Sbjct: 284 GVHVIPTITGHAYITAEARLCFDERDPFAWG 314 Lambda K H 0.319 0.139 0.403 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: 316 Number of extensions: 15 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: 335 Length of database: 318 Length adjustment: 28 Effective length of query: 307 Effective length of database: 290 Effective search space: 89030 Effective search space used: 89030 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 (21.7 bits) S2: 48 (23.1 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