Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase (NADPH) (EC 1.5.1.21) (characterized)
to candidate Ac3H11_4531 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::O54983 (313 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4531 Length = 353 Score = 106 bits (264), Expect = 9e-28 Identities = 84/267 (31%), Positives = 130/267 (48%), Gaps = 13/267 (4%) Query: 52 VAKHR--GFLGVMPAYSAAEDALTTKLVTFYEGHSNTAVPSHQASVLLFDPSNGSLLAVM 109 VA H G + +MP A + K V + ++ +P+ A +L D + G+ L + Sbjct: 53 VASHSRDGVIELMPI--ADGETYAFKYVNGHPKNTRWGLPTVMAFGVLADVATGAPLLLS 110 Query: 110 DGNVITAKRTAAVSAIATKLLKPPGSDVLCILGAGVQAYSHYEIFTEQFSFKEVRMWNRT 169 + + TA RTAA+SA+A + L PGS + ++G G Q+ F +R+++ Sbjct: 111 ELTLTTALRTAAMSAVAARALARPGSRTMALIGNGAQSEFQALAFHHLLGIDTLRLFDTD 170 Query: 170 RENAEKFASTVQGD---VRVCSSVQEAVTGADVIITVT--MATEPILFGEWVKPGAHINA 224 K + ++G C+S EAV GADV+ TVT IL + + PG HINA Sbjct: 171 PAATAKLQANLKGTGPRTVACTSTAEAVRGADVVTTVTADKTNATILTPDMLAPGMHINA 230 Query: 225 VGASRPDWRELDDELMRQAVLYVDSREAALKESGDVLLSGADI-FAELGEVISGAKPAHC 283 VG P EL +++RQA ++V+ E GD+ AD EL EV++G Sbjct: 231 VGGDCPGKTELHADVLRQAQVFVEYAPQTRIE-GDIQQLPADFAVTELWEVLAGQHGGRA 289 Query: 284 E--KTTVFKSLGMAVEDLVAAKLVYDS 308 TVF S+G A+ED A + + D+ Sbjct: 290 SDAAVTVFDSVGFALEDFSALRFLRDA 316 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: 12 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: 353 Length adjustment: 28 Effective length of query: 285 Effective length of database: 325 Effective search space: 92625 Effective search space used: 92625 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 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