Align proline racemase (EC 5.1.1.4) (characterized)
to candidate N515DRAFT_0959 N515DRAFT_0959 proline racemase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__Dyella79:N515DRAFT_0959 Length = 313 Score = 173 bits (439), Expect = 4e-48 Identities = 120/326 (36%), Positives = 168/326 (51%), Gaps = 19/326 (5%) Query: 6 SIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGS 65 +I IDSHT GE TR V+ G P++ ++ E++E + D R I EPRG + G+ Sbjct: 3 TIDVIDSHTGGEPTRTVIAGFPDLGAGTLMEQRERFRRDFDRWRAGIACEPRGSATVVGA 62 Query: 66 VMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGI 125 ++ P DA G+IF + YL MCGHGTIG + G + P H + E P G Sbjct: 63 LLLPPQSADACAGVIFFNNVSYLGMCGHGTIGVVRTLQHMG---RIGPGLHRI-ETPVGT 118 Query: 126 IRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGL 185 + ++ DG+ VS NV ++ + + V+V +PG G V DI++GG++F I + L L Sbjct: 119 VGAELH-ADGR---VSIDNVESYRHAKDVQVSVPGYGEVTGDIAWGGNWFFITKDTPLPL 174 Query: 186 KIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIF 245 I Q +LT +R + +E Q T A +D +EI P +N V+ Sbjct: 175 DIGHQR--ELTAYTEAIRRV----LEAQGITGAEGGEIDHIEI--NADLPGKAGRNFVLC 226 Query: 246 GQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVV 305 DRSPCGTGTSAKLA L A G+L GE + ESILG +G E T V Sbjct: 227 PGLAYDRSPCGTGTSAKLACLAADGKLAPGEVWRQESILG---EGSEFEATYTLGARGVK 283 Query: 306 PKITGSAYITGFNHFVIDEEDPLKHG 331 P+ITGSAY+ + + DE D G Sbjct: 284 PRITGSAYVVARSTLLFDEADAFTWG 309 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: 309 Number of extensions: 18 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: 313 Length adjustment: 28 Effective length of query: 307 Effective length of database: 285 Effective search space: 87495 Effective search space used: 87495 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