Align proline racemase (EC 5.1.1.4) (characterized)
to candidate H281DRAFT_01193 H281DRAFT_01193 4-hydroxyproline epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__Burk376:H281DRAFT_01193 Length = 323 Score = 178 bits (452), Expect = 1e-49 Identities = 114/332 (34%), Positives = 178/332 (53%), Gaps = 20/332 (6%) Query: 6 SIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGS 65 SI IDSHT GE TR+VV G P++ + E+ + + D++R ++ EPRG + M G+ Sbjct: 3 SITVIDSHTGGEPTRLVVEGGPDLGRGPLAERLDIFRRDFDHVRAGVVNEPRGSDVMVGA 62 Query: 66 VMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGI 125 ++ +P G+IF + GYL MCGHGTIG + + G ++P H + E P G+ Sbjct: 63 LLCEPHDTRCSAGVIFFNNVGYLGMCGHGTIGLIVSLAHMG---RIKPGVHRI-ETPVGV 118 Query: 126 IRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGL 185 + ++ DG VS NVPA+ Y+ V++D+PG+G V DI++GG++F ++ + G Sbjct: 119 VEAELH-GDG---SVSVRNVPAYRYRTEVQLDVPGLGRVHGDIAWGGNWFFLV--ADHGQ 172 Query: 186 KIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIF 245 +E N LT + +R +E T +D +E++ + T P +N V+ Sbjct: 173 TLEFANVESLTNVTWAIR----AALEANGITGEGGALIDHIELFADSTTPGVDSRNFVLC 228 Query: 246 GQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKG--EIVEETKVADFNA 303 DRSPCGTGTSAK+A L A L G + ESI+G++F+ E E+T NA Sbjct: 229 PGKAYDRSPCGTGTSAKIACLAADAHLAPGATWRQESIIGSIFEASYEPHEDTSHNVDNA 288 Query: 304 ----VVPKITGSAYITGFNHFVIDEEDPLKHG 331 V P I G+A+++ + +DP G Sbjct: 289 SRRYVRPSIRGTAHVSAEAKLIFSADDPFAWG 320 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: 287 Number of extensions: 13 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: 323 Length adjustment: 28 Effective length of query: 307 Effective length of database: 295 Effective search space: 90565 Effective search space used: 90565 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