Align proline racemase (EC 5.1.1.4) (characterized)
to candidate WP_025762974.1 X939_RS0109245 4-hydroxyproline epimerase
Query= BRENDA::A8DEZ8 (335 letters) >NCBI__GCF_000566685.1:WP_025762974.1 Length = 333 Score = 234 bits (598), Expect = 2e-66 Identities = 127/325 (39%), Positives = 188/325 (57%), Gaps = 4/325 (1%) Query: 10 IDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVMTQ 69 ID+HT G R+V GG P + G +M E++ + + D++R +M EPRGH+ M GS++ Sbjct: 8 IDAHTCGNPVRVVAGGGPLLLGANMMERRLHFLKEFDWIRKGLMFEPRGHDMMSGSILFP 67 Query: 70 PCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVV-PAVEPVTHVVMEAPAGIIRG 128 P P+ D G++F++ G L MCGHGTIG +T AIE G+V P V+ + +E PAG++ Sbjct: 68 PSDPENDIGVLFIETSGCLPMCGHGTIGTVTIAIEEGLVTPKVQ--GKLRLETPAGLVLV 125 Query: 129 DVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKIE 188 + K K V +NV ++L E + V+ P +G + D+++GG+F+AI+ I+ Sbjct: 126 EYQQEGKKVKSVKLVNVKSYLAAEKLSVECPDLGMLTVDVAYGGNFYAIVDPQCNFSGIQ 185 Query: 189 PQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIFGQG 248 A +L + R +NE HP HI + + P +T +N V +G Sbjct: 186 DYTADQLISWSRICRQRLNEAYSFVHPENKHINGLSHLLWTGAVIDPLSTARNAVFYGDK 245 Query: 249 QVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVVPKI 308 +DRSPCGTGTSA++A HA+G L VG+ F++ESI+G+ F G I E V A+VP I Sbjct: 246 AIDRSPCGTGTSARMAQWHAQGRLNVGDHFIHESIIGSKFVGTIENEATVGGKKAIVPAI 305 Query: 309 TGSAYITGFNHFVIDEE-DPLKHGF 332 G A +TG+N IDEE DP GF Sbjct: 306 EGWAVVTGYNTIFIDEEQDPYALGF 330 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: 290 Number of extensions: 12 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: 333 Length adjustment: 28 Effective length of query: 307 Effective length of database: 305 Effective search space: 93635 Effective search space used: 93635 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