Align proline racemase (EC 5.1.1.4) (characterized)
to candidate CA265_RS05710 CA265_RS05710 hydroxyproline-2-epimerase
Query= BRENDA::Q9L4Q3 (299 letters) >FitnessBrowser__Pedo557:CA265_RS05710 Length = 333 Score = 214 bits (544), Expect = 3e-60 Identities = 122/303 (40%), Positives = 174/303 (57%), Gaps = 6/303 (1%) Query: 1 MADKKKYLEDNLDYVRTALMHEPRGHNDMFGSIITSSNNKEADFGIIFMDGGGYLNMCGH 60 M++K+++ D++RT LM EPRGH+ M GSI+ ++ D ++F++ G L MCGH Sbjct: 32 MSEKRQHFLKEFDWIRTGLMFEPRGHDMMSGSILYPPHDPANDVAVLFIETSGCLPMCGH 91 Query: 61 GSIGAATVAVETGMVEMVEPVTNINMEAPAGLIKAKVMVENEKVKEVSITNVPSFLYMED 120 G+IG T+A+E G+++ P I MEAPAGL+ + E +KVK V + NV S+L E+ Sbjct: 92 GTIGTITIAIEEGLIQPKIPGV-IRMEAPAGLVLIEYKQEGKKVKSVKLKNVASYLAAEN 150 Query: 121 AKLEVPSLNKTITFDISFGGSFFAIIHAKELGVKVETSQVDVLKKLGIEIRDLINEKIKV 180 +E P L T+TFD+++GG+F+AI+ +E +E L IR INE+ Sbjct: 151 LSVECPDLG-TLTFDVAYGGNFYAIVDPQENFPGLENYTASQLITWSQTIRKRINEQYTF 209 Query: 181 QHPELEHIKTVDLVEIYDEPSNPEATYKNVVIFGQGQVDRSPCGTGTSAKLATLYKKGHL 240 HP I V + +P +T +N V +G +DRSPCGTGTSA+LA Y KG L Sbjct: 210 VHPLDPTINGCSHVLWTGKTIDPTSTARNAVFYGDKAIDRSPCGTGTSARLAQWYAKGKL 269 Query: 241 KIDEKFVYESITGTMFKGRVLEETKVGEFDAIIPEITGGAYITGFNHFVI----DPLKYG 296 K E F++ES G+ F GRV E + AIIP + G A I G+N I DP +G Sbjct: 270 KQGEDFIHESFIGSKFIGRVEEVVDLNGIKAIIPSVEGWAKIYGYNTIKIDAEDDPYAHG 329 Query: 297 FTV 299 F V Sbjct: 330 FQV 332 Lambda K H 0.317 0.137 0.388 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: 258 Number of extensions: 15 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: 299 Length of database: 333 Length adjustment: 27 Effective length of query: 272 Effective length of database: 306 Effective search space: 83232 Effective search space used: 83232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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