Align proline racemase (EC 5.1.1.4) (characterized)
to candidate AO353_14925 AO353_14925 hydroxyproline-2-epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__pseudo3_N2E3:AO353_14925 Length = 311 Score = 199 bits (505), Expect = 1e-55 Identities = 119/327 (36%), Positives = 183/327 (55%), Gaps = 20/327 (6%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 + I +DSHT GE TR+V+ G P + SM E+K L E D+ RTA +LEPRG + + G Sbjct: 2 KRIHVLDSHTGGEPTRLVIAGFPELGSGSMAERKRRLAEEHDHWRTATVLEPRGSDVLVG 61 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124 +++ +P P+A G+IF + GYL MCGHGTIG + + + +EP H + E P G Sbjct: 62 ALLCEPQDPEACAGVIFFNNSGYLGMCGHGTIGLVAS---LAYLERIEPGVHRI-ETPVG 117 Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184 + + + + VS NVPA+ Y++ V + LPG GT DI++GG++F +I + G Sbjct: 118 TVEATL----HEDRSVSVRNVPAYRYRKAVPLTLPGYGTASGDIAWGGNWFFLI--ADHG 171 Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244 +I N LT +R E +E Q +D +E++ + P A +N V+ Sbjct: 172 QRIASDNLEALTAYTWAVR----EALENQGIRGEDGGEIDHIELFAD--DPVADSRNFVL 225 Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304 DRSPCGTGTSAKLA L A G+L+ GE + S++G+ F+ + D + Sbjct: 226 CPGKAYDRSPCGTGTSAKLACLAADGKLQPGEVWRQASVIGSQFEASY----ERLDEQRI 281 Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHG 331 +P I G A+++G +H +++E+DP G Sbjct: 282 IPTIRGRAHMSGESHLLLEEDDPFVWG 308 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: 297 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: 311 Length adjustment: 28 Effective length of query: 307 Effective length of database: 283 Effective search space: 86881 Effective search space used: 86881 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