Align proline racemase (EC 5.1.1.4) (characterized)
to candidate RR42_RS36345 RR42_RS36345 hydroxyproline-2-epimerase
Query= BRENDA::B8LFE4 (345 letters) >FitnessBrowser__Cup4G11:RR42_RS36345 Length = 322 Score = 176 bits (445), Expect = 1e-48 Identities = 119/337 (35%), Positives = 171/337 (50%), Gaps = 31/337 (9%) Query: 7 MTCIDMHTAGEPARIVTSGFPNIPGASLVEKRDHLQRHMDHIRRRVMLEPRGHDNMFGAF 66 M ID HT GEP R+V GFP++ AS+ + D L R DH R +LEPRG D M GA Sbjct: 1 MRVIDSHTGGEPTRLVIDGFPDLGRASMAARLDRLAREYDHWRAATVLEPRGSDVMVGAL 60 Query: 67 LFYPLTDGADFSVIFMDAGGYLNMCGHNSIAIATAAVEMGMVHPTPDASQMPLVLDTPAG 126 L P++ A VIF + GYL MCGH +I + + +G + P +DTP G Sbjct: 61 LCPPVSADACAGVIFFNNSGYLGMCGHGTIGLVASLAHLGRIAPGRHR------IDTPVG 114 Query: 127 RVLTDVHLEWNKGVCEVHHVAVKNVPSFLYMQDIVVELPHPYGKVTVDISFGGSFFALID 186 V +H E V V+NVP++ Y + V++P +G+VT DI++GG++F L + Sbjct: 115 TVEATLH--------EDGSVGVRNVPAWRYRHAVAVDVP-GHGRVTGDIAWGGNWFFLTE 165 Query: 187 AAQLQLTVDKGHLSTLQHVGGLLRDTLNRNVSVQHPQLPHINRIDCVEIYDPPTN-PAAS 245 + + +++ +L L +R L R PH +D +E++ P A Sbjct: 166 SHGQR--IERDNLDALTAFAWAVRQALER----AGIAAPHGAPVDHIELFCTPDGADDAD 219 Query: 246 CKNVVIFGNSQVDRSPCGTGTCAKMALLYAKGKLKVGDTFVHESISGTLF--HGKLLNQV 303 +N V+ DRSPCGTGT AK+A L A GKL G + S++G+ F H N+ Sbjct: 220 SRNFVLCPGKAYDRSPCGTGTSAKLACLAADGKLAPGTPWRQASVTGSRFVAHYAPANE- 278 Query: 304 SMPGVKYPAVISEISGSAYITGFNTLLFAPRDPFRDG 340 PG +I + G A++ TLL A DPF G Sbjct: 279 --PG----RIIPTVHGHAHVYAEATLLIAHDDPFAWG 309 Lambda K H 0.323 0.139 0.427 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: 326 Number of extensions: 20 Number of successful extensions: 7 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: 345 Length of database: 322 Length adjustment: 28 Effective length of query: 317 Effective length of database: 294 Effective search space: 93198 Effective search space used: 93198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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