Align proline racemase (EC 5.1.1.4) (characterized)
to candidate AO356_24960 AO356_24960 hydroxyproline-2-epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24960 Length = 310 Score = 187 bits (475), Expect = 3e-52 Identities = 113/327 (34%), Positives = 180/327 (55%), Gaps = 21/327 (6%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 + I IDSHT GE TR+V G P++ SM E+K+ L D RTA +LEPRG + + G Sbjct: 2 KRITVIDSHTGGEPTRLVTDGFPDLGQGSMAERKQRLAAEHDTWRTACVLEPRGSDVLVG 61 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124 +++ +P P A G+IF + GYL MCGHGTIG + + G + P H + E P G Sbjct: 62 ALLCEPVDPSACAGVIFFNNSGYLGMCGHGTIGLVASLAHLG---RIGPGVHSI-ETPVG 117 Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184 ++ + + + VS NVPA+ Y++ + +++PG+G V D+++GG++F +I ++ G Sbjct: 118 TVQATL----HEDRSVSVRNVPAYRYRKALALEVPGIGQVVGDVAWGGNWFFLI--AEHG 171 Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244 ++ N LT + + +E Q +D +E++ + P+A +N V+ Sbjct: 172 QRVAGDNLDALTAYTY----AVQQALEQQGFRGEDGGLIDHIELFAD--DPQADSRNFVL 225 Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304 DRSPCGTGTSAKLA L A G+L+ G+ + S++G+ F+G + + Sbjct: 226 CPGKAYDRSPCGTGTSAKLACLAADGKLQPGQIWRQASVIGSEFEGSYEHSGE-----RI 280 Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHG 331 VP I G AYI+ +I+ +DP G Sbjct: 281 VPTIRGRAYISAETTLIIETDDPFAWG 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: 281 Number of extensions: 10 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: 310 Length adjustment: 28 Effective length of query: 307 Effective length of database: 282 Effective search space: 86574 Effective search space used: 86574 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