Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate AZOBR_RS03120 AZOBR_RS03120 ornithine cyclodeaminase
Query= BRENDA::Q485R8 (316 letters) >FitnessBrowser__azobra:AZOBR_RS03120 Length = 318 Score = 200 bits (508), Expect = 4e-56 Identities = 117/313 (37%), Positives = 175/313 (55%), Gaps = 5/313 (1%) Query: 1 MKIISAEQVHQNLNFEELIPLLKQSFSRPFSMPQRQVYSLAPEQSENHDAFALLPSWN-E 59 M+ ++ ++ L+F LI ++Q+F +P R +++ ++ L+P+W Sbjct: 1 MRTVTGAELKSVLHFRMLIERMRQTFRAGVEVPMRHHHTVET-YGQSDGTLLLMPAWQVN 59 Query: 60 EVIGNKAFTYFPDNAKKHDLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALASQ 119 + IG K T FPDN K DLP + +L +TG P A++DGT++T RTAA SALA+ Sbjct: 60 QSIGVKVVTVFPDNGAK-DLPAVQGLYLLMDGKTGMPQAVLDGTALTKRRTAAASALAAS 118 Query: 120 LLSRKNSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPAVT 179 L+R +S+ L++ GTG LA L++A TV IK V +WGR+ +K K+ + F P Sbjct: 119 YLARPDSERLLMVGTGALAPELIEAFATVLPIKHVLVWGRSLEKAKKVASRFH--RPKFR 176 Query: 180 FKTSVDVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTILRA 239 + + D+ V A +I CAT AK PL G + G H+D +G + RE D I R+ Sbjct: 177 IEATADLEGAVRGAQVISCATLAKEPLIRGEWLQPGAHLDLVGGFTPEMREADDDCIRRS 236 Query: 240 RVFVDSLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSVGT 299 RVFVD+ EAG+++ PM +I G+L D+ + R+ D+ITLFKSVGT Sbjct: 237 RVFVDTREGACKEAGDIVQPMKAGILTDADIAGDLYDLTRGQRAGRRFYDQITLFKSVGT 296 Query: 300 AISDLVAAHSVVE 312 A+ DL AA VE Sbjct: 297 ALEDLCAAQLAVE 309 Lambda K H 0.318 0.131 0.379 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: 201 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: 316 Length of database: 318 Length adjustment: 27 Effective length of query: 289 Effective length of database: 291 Effective search space: 84099 Effective search space used: 84099 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 (21.8 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