Align proline racemase (EC 5.1.1.4) (characterized)
to candidate SM_b20270 SM_b20270 proline racemase
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__Smeli:SM_b20270 Length = 342 Score = 187 bits (474), Expect = 4e-52 Identities = 102/337 (30%), Positives = 181/337 (53%), Gaps = 5/337 (1%) Query: 1 MKFSRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHN 60 M+ +++I I +H GE ++VGG+ G+++ E+ ++ LR ++ EPRG Sbjct: 1 MRSTKTIHVISAHAEGEVGDVIVGGVAPPPGDTIWEQSRWIARE-QTLRNFVLNEPRGGV 59 Query: 61 DMFGSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVME 120 +++ P PDAD I M+ M G +I T +++G++P EPVT + +E Sbjct: 60 FRHVNLLVPPKHPDADAAFIIMEPEDTPPMSGSNSICVSTVLLDSGILPMKEPVTEITLE 119 Query: 121 APAGIIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHA 180 AP G++R DGKA+ + N+P+F + ++++ G+GT+ D ++GG F I+ A Sbjct: 120 APGGLVRVRAECRDGKAERIFVENLPSFAERLDAKLEVEGLGTLTVDTAYGGDSFVIVDA 179 Query: 181 SQLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYK 240 + +G ++P A + L +++ + N K+ HP + ++ P A Sbjct: 180 AAMGFALKPDEAHDIARLGVRITNAANAKLGFHHPENPDWRHFSFC-LFAGPVERTAEGL 238 Query: 241 N---VVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETK 297 V G+VDRSP GT SA++A LHA+G++ + ++ S++G+ F G I+ T+ Sbjct: 239 RAGAAVAIQPGKVDRSPTGTALSARMAVLHARGQMGLSDRLTAVSLIGSTFSGRILGTTE 298 Query: 298 VADFNAVVPKITGSAYITGFNHFVIDEEDPLKHGFIL 334 V AV+P+I+G A+ITG + ++D DP G+ L Sbjct: 299 VGGRPAVLPEISGRAWITGTHQHMLDPSDPWPEGYRL 335 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: 269 Number of extensions: 15 Number of successful extensions: 3 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: 342 Length adjustment: 28 Effective length of query: 307 Effective length of database: 314 Effective search space: 96398 Effective search space used: 96398 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