Align proline racemase (EC 5.1.1.4) (characterized)
to candidate 5209913 Shew_2361 proline racemase (RefSeq)
Query= BRENDA::A8DEZ8 (335 letters) >FitnessBrowser__PV4:5209913 Length = 346 Score = 232 bits (591), Expect = 1e-65 Identities = 120/334 (35%), Positives = 195/334 (58%), Gaps = 11/334 (3%) Query: 8 QAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVM 67 + +D+HT GE RI++ G P I G+++ K+ YL +LD R +M EPRGH DM+G+++ Sbjct: 18 KTLDAHTEGEPLRILLEGYPEIPGDTILAKRRYLTAHLDQYRKLLMHEPRGHADMYGAII 77 Query: 68 TQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIR 127 T P ADFG++F+ GY +MCGHG + +T A+ETG + + + ++APAG+I Sbjct: 78 TAPITTGADFGVLFLHNEGYSSMCGHGILALVTVAVETGTLALGDTPREIKIDAPAGLIH 137 Query: 128 GDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKI 187 + +VSF NVP++ V + G+G V +DI FGG+++A + A LGL Sbjct: 138 AKAYRDETGELKVSFRNVPSWAEALDCRVTVEGIGEVAYDIGFGGAYYAYVDADGLGLSC 197 Query: 188 EPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIY------DEPTHPEATYKN 241 P+N +L + + I + QHP LAH DL +Y + + +A ++ Sbjct: 198 APENVAQLIDWGRR----IKHAVMAQHP-LAHPLEADLGFLYGTIFTSSKTSSNDAHSRH 252 Query: 242 VVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADF 301 V +F G+VDRSP GTG + ++A LHA+GE+ +GE+ ESI+ + ++ Sbjct: 253 VCVFADGEVDRSPTGTGVAGRIALLHARGEVALGERLRIESIVDGAMQVCALDNADFYGK 312 Query: 302 NAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335 AV+P+++G A+ITG + F++D +D + GF+L+ Sbjct: 313 AAVIPEVSGRAFITGRHEFILDPKDQFQQGFMLR 346 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: 346 Number of extensions: 18 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: 346 Length adjustment: 28 Effective length of query: 307 Effective length of database: 318 Effective search space: 97626 Effective search space used: 97626 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