Align proline racemase (EC 5.1.1.4) (characterized)
to candidate PfGW456L13_3147 4-hydroxyproline epimerase (EC 5.1.1.8)
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3147 Length = 332 Score = 236 bits (601), Expect = 8e-67 Identities = 127/330 (38%), Positives = 185/330 (56%), Gaps = 1/330 (0%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 RS +DSH G R+V GG P + SM E++E D++RTA+M EPRGH+ M G Sbjct: 3 RSFFCVDSHACGNPVRVVTGGGPLLPSVSMAERREIFVREHDWVRTALMFEPRGHDIMSG 62 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124 ++ D DFG +F++ G L MCG GTIG T IE G+V EP + +E PAG Sbjct: 63 VIIYPSSREDCDFGALFIEVSGCLPMCGAGTIGLSTVVIEEGLVTPREP-GRLAIETPAG 121 Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184 + D T+ + NV ++L+ V VD+PGVG + DI++GG+F+A++ + Sbjct: 122 RVDVDYTMNGEYVDSIRLFNVASYLHSADVVVDVPGVGELVVDIAYGGNFYAVVEPQENW 181 Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244 + + L+ KLR + E + HP + I V V DE A + V Sbjct: 182 PGLNGLTTADIVSLSQKLRAALAEVSDPVHPENSRISGVHHVIWSDEEHSTAADGRGAVF 241 Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304 +G +DRSP GTGTSA++A L KG LK+G+ + ES++GT+F+G++ KV F+ + Sbjct: 242 YGDKAIDRSPGGTGTSARMAQLFGKGRLKIGDTYRNESLIGTIFEGKVEASVKVGTFDGI 301 Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHGFIL 334 P I G A ITG N +D++DPL+HGF L Sbjct: 302 RPSIGGWAQITGHNTIFVDDKDPLRHGFQL 331 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: 319 Number of extensions: 14 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: 335 Length of database: 332 Length adjustment: 28 Effective length of query: 307 Effective length of database: 304 Effective search space: 93328 Effective search space used: 93328 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: 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