Align proline racemase (EC 5.1.1.4) (characterized)
to candidate 5209915 Shew_2363 proline racemase (RefSeq)
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__PV4:5209915 Length = 333 Score = 246 bits (628), Expect = 6e-70 Identities = 124/323 (38%), Positives = 193/323 (59%), Gaps = 1/323 (0%) Query: 10 IDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVMTQ 69 +D+HT G R+V G P++KG +M EK++ D++R A+M EPRGH+ M G+ + Sbjct: 9 VDAHTCGNPVRLVTSGHPDLKGRTMSEKRQDFLAQYDWIRKALMFEPRGHDMMSGAFLYP 68 Query: 70 PCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIRGD 129 PC +AD I+F++ G L MCGHGTIG +TAA+E+G++ P + ++ PAG I+ Sbjct: 69 PCSDNADAAILFIETSGCLPMCGHGTIGTITAALESGLLTPKMP-GQLTIDVPAGQIKVQ 127 Query: 130 VTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKIEP 189 K V NVPA+L + V +D+PG+G +K D+S+GG+++AI+ + Sbjct: 128 YQQTGAKVDWVKIFNVPAYLAHKDVVLDIPGLGPLKIDVSYGGNYYAIVDPQANFPGLRH 187 Query: 190 QNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIFGQGQ 249 +AG + + +R++ + ++ HP + V V + + N V +G Sbjct: 188 WSAGDILRWSPIVREVAHRELNCVHPDDPTVNGVSHVLWTGDTISEGSNGANAVFYGDKA 247 Query: 250 VDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVVPKIT 309 +DRSPCGTGTSA+LA L+++GELKVG+++ +ESI+G+ F G I TKV F+A++P I Sbjct: 248 IDRSPCGTGTSARLAQLYSRGELKVGDEYTHESIIGSQFVGRIEAATKVGAFDAIMPSIK 307 Query: 310 GSAYITGFNHFVIDEEDPLKHGF 332 G A ITG N +D+ DP GF Sbjct: 308 GWARITGHNAITVDDNDPYAFGF 330 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: 317 Number of extensions: 11 Number of successful extensions: 3 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