Align proline racemase (EC 5.1.1.4) (characterized)
to candidate PP_1258 PP_1258 4-hydroxyproline epimerase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__Putida:PP_1258 Length = 308 Score = 203 bits (517), Expect = 4e-57 Identities = 124/328 (37%), Positives = 183/328 (55%), Gaps = 23/328 (7%) Query: 5 RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64 + I IDSHT GE TR+V+ G P ++G SM E+++ L E D R A +LEPRG++ + G Sbjct: 2 KQIHVIDSHTGGEPTRLVMKGFPQLRGRSMAEQRDELRELHDRWRRACLLEPRGNDVLVG 61 Query: 65 SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVV-PAVEPVTHVVMEAPA 123 ++ P DA G+IF + GYLNMCGHGTIG + + G++ P V + V Sbjct: 62 ALYCPPVSADATCGVIFFNNAGYLNMCGHGTIGLVASLQHMGLITPGVHKIDTPV----- 116 Query: 124 GIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQL 183 G V+ + ++ NVP++ Y++ V VD+PG G V+ DI++GG++F ++ S+ Sbjct: 117 ----GQVSATLHEDGAITVANVPSYRYRQQVAVDVPGHGVVRGDIAWGGNWFFLV--SEH 170 Query: 184 GLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVV 243 G +IE N LTE + + +E Q T + +D +E++ + P A +N V Sbjct: 171 GQRIELDNREALTEYTWAML----KALETQGVTGENGAPIDHIELFAD--DPNADSRNFV 224 Query: 244 IFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNA 303 + DRSPCGTGTSAKLA L A G+L G+ +V SI G+ F G D Sbjct: 225 MCPGKAYDRSPCGTGTSAKLACLAADGKLAEGQTWVQASITGSQFHGRYAR-----DGER 279 Query: 304 VVPKITGSAYITGFNHFVIDEEDPLKHG 331 + P ITG AY+T + +IDE+DP G Sbjct: 280 IRPFITGRAYMTADSTLLIDEQDPFAWG 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: 11 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: 308 Length adjustment: 28 Effective length of query: 307 Effective length of database: 280 Effective search space: 85960 Effective search space used: 85960 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