Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate BPHYT_RS21000 BPHYT_RS21000 ornithine cyclodeaminase
Query= BRENDA::O54983 (313 letters) >FitnessBrowser__BFirm:BPHYT_RS21000 Length = 304 Score = 130 bits (328), Expect = 3e-35 Identities = 96/304 (31%), Positives = 147/304 (48%), Gaps = 25/304 (8%) Query: 15 DHLRSSSLL---IPPLEAALANFSKGPDGGVMQPVRTVVPVAKHRGFLGVMPAYSAAEDA 71 DH+R + I L ALA G PV+ V + +M A + Sbjct: 7 DHVRRLITMRDAIAELRIALAEHGAG-----RAPVQPRVRTKGEHVSVSMMGAILPSRGV 61 Query: 72 LTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVMDGNVITAKRTAAVSAIATKLLK 131 K+ + + G + VP LF +G L++++ G+ +T RTAAV+ IA+ L Sbjct: 62 CGAKVYSTHGGRFDFVVP-------LFSSDDGCLISILHGDALTEFRTAAVTRIASDALA 114 Query: 132 PPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMW--NRTRENAEKFASTVQGDVRVCSS 189 PG+ VL + G G QA +H + S + V + + + + + + S Sbjct: 115 RPGARVLAVFGTGRQARAHIRALADGSSIERVLIVGIDHVAQTVAEMQALFPDKLIEASH 174 Query: 190 VQEAVTGADVIITVTMATEPILFGEWVKPGAHINAVGASRPDWRELDDELMRQA-VLYVD 248 Q A ADVI+T T + P+ G WVKPG I A+G+S+PD RELDD L+ +A L V+ Sbjct: 175 AQAAARAADVIVTATRSATPLFDGTWVKPGVFIAAIGSSKPDARELDDALLARANTLVVE 234 Query: 249 SREAALKESGDVLLSGADIFA-----ELGEVISGAK--PAHCEKTTVFKSLGMAVEDLVA 301 S E A E+GD+L++ + A ELG V++ + P T+FKSLG + D+ Sbjct: 235 SLEQARSEAGDLLMAAPGVVAWDDIIELGAVLANRRIEPRARGDVTIFKSLGFGLADVAL 294 Query: 302 AKLV 305 A L+ Sbjct: 295 AGLI 298 Lambda K H 0.316 0.131 0.376 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: 221 Number of extensions: 13 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: 313 Length of database: 304 Length adjustment: 27 Effective length of query: 286 Effective length of database: 277 Effective search space: 79222 Effective search space used: 79222 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 (21.7 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