Align proline racemase (EC 5.1.1.4) (characterized)
to candidate Ac3H11_4170 4-hydroxyproline epimerase (EC 5.1.1.8)
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4170 Length = 314 Score = 172 bits (435), Expect = 1e-47 Identities = 112/331 (33%), Positives = 174/331 (52%), Gaps = 19/331 (5%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 + IQ +DSHT GE TR+V+GG P++ SM E++E L D R A +LEPRG + + G Sbjct: 2 KRIQILDSHTGGEPTRLVIGGFPDLGAGSMAERRERLAREHDAWRAATVLEPRGSDVVVG 61 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124 +++ P P G+IF + GYL MCGHGTIG + + G ++P H + E P G Sbjct: 62 ALLCTPQDPANAAGVIFFNNSGYLGMCGHGTIGLVASLAYMG---RIQPGEHRI-ETPVG 117 Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184 + + DG VS NVPA+ + VD+PG G V D+++GG++F +I S G Sbjct: 118 TVTTTLH-TDG---SVSVRNVPAYRLHHQLAVDVPGYGRVVGDVAWGGNWFFLI--SDHG 171 Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIY-DEPTHPEATYKNVV 243 ++ N E M + + ++ Q + +D +E++ D+ A +N V Sbjct: 172 QRVTSDN----LEALMHYSCAVQQALKDQGIRGDNGGEIDHIELFADDEAEEPADSRNYV 227 Query: 244 IFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNA 303 + DRSPCGTGTSAK+A L A G+L G + SI+G+ F+ + D Sbjct: 228 LCPGKAYDRSPCGTGTSAKIACLAADGKLAPGAVWRQASIIGSQFEASYT----LQDDGK 283 Query: 304 VVPKITGSAYITGFNHFVIDEEDPLKHGFIL 334 ++P + G A+++ +I++ DP G L Sbjct: 284 LIPTLRGRAHMSAEATLLIEDSDPFGWGIRL 314 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: 13 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: 314 Length adjustment: 28 Effective length of query: 307 Effective length of database: 286 Effective search space: 87802 Effective search space used: 87802 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