Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate AO353_25185 AO353_25185 ornithine cyclodeaminase
Query= BRENDA::O54983 (313 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25185 Length = 350 Score = 106 bits (264), Expect = 9e-28 Identities = 82/260 (31%), Positives = 131/260 (50%), Gaps = 12/260 (4%) Query: 57 GFLGVMPAYSAAEDALTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVMDGNVITA 116 G + +MP + + K V + G+ + + A +L D +G + + + TA Sbjct: 53 GVIELMPTDDGQQYSF--KYVNGHPGNGQRDLLTVMAFGVLADVHSGYPTLLSELTLTTA 110 Query: 117 KRTAAVSAIATKLLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRTRENAEKF 176 RTAA SA+ + L PG+ V+ I+G G Q+ F E S +E+R+++ R+ + K Sbjct: 111 VRTAATSALVAQSLARPGASVMAIIGNGAQSEFQAIAFHEMLSIREIRIFDIDRDASLKL 170 Query: 177 ASTVQG----DVRVCSSVQEAVTGADVIITVT--MATEPILFGEWVKPGAHINAVGASRP 230 + +V + SSVQEAV GA ++ TVT A IL E ++PG HINAVG P Sbjct: 171 KHNLSAFPGIEVILSSSVQEAVKGAHIVTTVTADKAYATILTPEMIEPGMHINAVGGDCP 230 Query: 231 DWRELDDELMRQAVLYVDSREAALKESGDVLLSGADI-FAELGEVISGAKPA--HCEKTT 287 EL E++R A + V+ E + GD+ AD E ++ G P + + T Sbjct: 231 GKTELHAEILRNARIIVEF-EPQTRIEGDIQQLEADSPVVEFFRIVLGEVPGRENDAQVT 289 Query: 288 VFKSLGMAVEDLVAAKLVYD 307 VF S+G A+ED + + ++D Sbjct: 290 VFDSVGFALEDFSSLRYLHD 309 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: 232 Number of extensions: 14 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: 350 Length adjustment: 28 Effective length of query: 285 Effective length of database: 322 Effective search space: 91770 Effective search space used: 91770 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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