Align proline racemase (EC 5.1.1.4) (characterized)
to candidate SM_b20268 SM_b20268 hydroxyproline-2-epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__Smeli:SM_b20268 Length = 333 Score = 283 bits (724), Expect = 4e-81 Identities = 141/334 (42%), Positives = 214/334 (64%), Gaps = 5/334 (1%) Query: 4 SRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMF 63 + + ID HT G R+V GG P ++G +M EK+ + + D++RT +M EPRGH+ M Sbjct: 3 THTFSCIDGHTCGNPVRLVSGGGPRLEGANMLEKRAHFLKEFDWIRTGLMFEPRGHDMMS 62 Query: 64 GSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPA 123 GS++ P PD D ++F++ G L MCGHGTIG +T IE G++ EP + ++APA Sbjct: 63 GSILYPPTRPDCDVAVLFIETSGCLPMCGHGTIGTITMGIENGLITPREP-GKLSIDAPA 121 Query: 124 GIIRGDVTV-VDGK-AKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHAS 181 G + D+T +G+ +EV NVP+FLY EG+ ++ G+G + D+++GG+F+AI+ Sbjct: 122 GKV--DITYRQEGRFVEEVRLTNVPSFLYAEGLAAEVEGLGEIVVDVAYGGNFYAIVEPQ 179 Query: 182 QLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKN 241 + + AG+L + KLR +N K E HP I+ + ++ +PT PEA +N Sbjct: 180 KNFRDMADHTAGELVGWSPKLRAALNAKYEFVHPEHPEIRGLSHIQWTGKPTQPEAHARN 239 Query: 242 VVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADF 301 V +G+ +DRSPCGTGTSA++A L AKG+LKVG++FV+ESI+G+LFKG + KVAD Sbjct: 240 AVFYGEKAIDRSPCGTGTSARIAQLAAKGKLKVGDEFVHESIIGSLFKGRVEAAAKVADR 299 Query: 302 NAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335 +A++P I G A +TG N ID+ DP HGF+++ Sbjct: 300 DAIIPSIAGWARMTGINTIFIDDRDPFAHGFVVR 333 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: 342 Number of extensions: 12 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: 333 Length adjustment: 28 Effective length of query: 307 Effective length of database: 305 Effective search space: 93635 Effective search space used: 93635 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