Align proline racemase (EC 5.1.1.4) (characterized)
to candidate GFF2804 PS417_14305 hydroxyproline-2-epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__WCS417:GFF2804 Length = 308 Score = 179 bits (454), Expect = 8e-50 Identities = 116/327 (35%), Positives = 175/327 (53%), Gaps = 21/327 (6%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 + + IDSHT GE TR+V+ G P + G ++ ++ L D R A +LEPRG++ + G Sbjct: 2 KRLHVIDSHTGGEPTRLVMSGFPALSGATIADQLHSLRTEHDQWRRACLLEPRGNDVLVG 61 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124 ++ +P P A G+IF + GYL MCGHGTIG + + G ++P H + + P G Sbjct: 62 ALYCEPVTPGAICGVIFFNNAGYLGMCGHGTIGLVASLHHLG---RIQPGVHTI-DTPVG 117 Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184 + + DG V+ NVPA+ + V V++PG G V DI++GG++F ++ S G Sbjct: 118 PVAATLH-EDG---AVTLRNVPAYRLHQQVPVEVPGHGVVYGDIAWGGNWFFLV--SDHG 171 Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244 +++ N LT+ + + +E Q A +D +E++ + ++ +N V+ Sbjct: 172 QRLQMDNVDALTDYTWAML----KALEDQGIHGADGALIDHIELFADDDRADS--RNFVM 225 Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304 DRSPCGTGTSAKLA L A G LK GE + SI G+ F G D V Sbjct: 226 CPGKAYDRSPCGTGTSAKLACLAADGTLKPGETWTQASITGSQFDGHY-----EWDGERV 280 Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHG 331 P ITG+AY+T + +IDE DP G Sbjct: 281 RPFITGNAYMTADSTLLIDERDPFAWG 307 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: 283 Number of extensions: 12 Number of successful extensions: 5 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: 308 Length adjustment: 28 Effective length of query: 307 Effective length of database: 280 Effective search space: 85960 Effective search space used: 85960 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