Align proline racemase (EC 5.1.1.4) (characterized)
to candidate WP_085216990.1 B9N75_RS00310 4-hydroxyproline epimerase
Query= BRENDA::A8DEZ8 (335 letters) >NCBI__GCF_900177405.1:WP_085216990.1 Length = 332 Score = 243 bits (619), Expect = 6e-69 Identities = 129/323 (39%), Positives = 185/323 (57%), Gaps = 1/323 (0%) Query: 10 IDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVMTQ 69 ID HTAG R+V GG P ++G SM E++ E D++RT + EPRGH M G + Sbjct: 8 IDGHTAGNPVRLVAGGAPPLRGASMAERRLDFLERFDWIRTGLCFEPRGHAMMSGGFLYP 67 Query: 70 PCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIRGD 129 P D+D GI+F++ G L MCGHGTIG +T +E G++ E + +E PAGII Sbjct: 68 PTRDDSDCGILFIETSGSLPMCGHGTIGMVTFGLENGLITPRE-AGGLRIEVPAGIIDIA 126 Query: 130 VTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKIEP 189 + + V NVPA+L ++ +E+D+PG G + D+++GG+++AI+ ++ Sbjct: 127 YRTDGDRVRSVRIHNVPAYLARQALEIDVPGFGPLTVDVAYGGNYYAIVEPQGAYTGLDD 186 Query: 190 QNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIFGQGQ 249 A +L L+ +R+ + E HP A I+ V V D P A +N V +G Sbjct: 187 LGAERLVALSRIVREQVRAAYEPVHPLDASIRGVSHVLWADAPKGDGADGRNAVFYGDSA 246 Query: 250 VDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVVPKIT 309 +DRSPCGTGTSA+LA L G L VG+ FV+ES +G+ F G + E +V + A+VP I Sbjct: 247 IDRSPCGTGTSARLAQLAGTGRLSVGDAFVHESYIGSRFTGRVEAEARVGELPAIVPSIE 306 Query: 310 GSAYITGFNHFVIDEEDPLKHGF 332 GSA TG+N ID EDP GF Sbjct: 307 GSAIATGYNTIWIDREDPFWAGF 329 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: 331 Number of extensions: 17 Number of successful extensions: 2 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: 332 Length adjustment: 28 Effective length of query: 307 Effective length of database: 304 Effective search space: 93328 Effective search space used: 93328 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 24 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