Align 3-keto-5-aminohexanoate cleavage enzyme (EC 2.3.1.247) (characterized)
to candidate PP_0303 PP_0303 dehydrocarnitine cleavage enzyme
Query= BRENDA::Q8RHX2 (272 letters) >FitnessBrowser__Putida:PP_0303 Length = 294 Score = 184 bits (468), Expect = 1e-51 Identities = 113/295 (38%), Positives = 169/295 (57%), Gaps = 25/295 (8%) Query: 1 MMEKLIITAAICGAEVTKEHNPAVPYTVEEIAREAESAYKAGASIIHLHVREDD-GTPTQ 59 M +IIT A+ GA T + VP T ++IA A A KAGA+++H HVR+ G ++ Sbjct: 1 MNHDVIITCALTGAGDTASKSHLVPVTPKQIAESAVEAAKAGATVVHCHVRDPQTGRFSR 60 Query: 60 DKERFRKCIEAIREKCPDVIIQPSTG------------------GAVGMTDLERLQPTE- 100 D +R+ +E IRE D+I+ + G G + LERL E Sbjct: 61 DVALYREVMERIREADVDIIVNLTAGMGGDLEIGPGETPLAFGPGTDLIGPLERLAHVEA 120 Query: 101 LHPEMATLDCGTCNFG-GDEIFVNTENTIKNFGKILIERGVKPEIEVFDKGMIDYAIRYQ 159 L PE+ TLDCGT NFG G+ I+V+T ++ K + E GVK E+E+FD G + +A + Sbjct: 121 LLPEICTLDCGTLNFGDGNSIYVSTPAQLRAGAKRITELGVKAELEIFDTGHLWFAKQMM 180 Query: 160 KQGFIQKPMHFDFVLGVQMSASARDLVF--MSESIPEGSTWTVAGVGRHQFQMAALAIVM 217 K+G ++ P+ F LG+ A A M +++P TW G+GR Q MAA A+++ Sbjct: 181 KEGLLEDPL-FQLCLGIPWGAPADTTTMKAMVDNLPANVTWAGFGIGRMQMPMAAQAVLL 239 Query: 218 GGHVRVGFEDNVYIDKGILAKSNGELVERVVRLAKELGREIATPDEARQILSLKK 272 GG+VRVG EDN+Y+D+G+LA SNG+LVER + +G + +P E R+ ++LK+ Sbjct: 240 GGNVRVGLEDNLYLDRGVLA-SNGQLVERASEIITRMGGRVLSPAEGREKMNLKR 293 Lambda K H 0.319 0.137 0.394 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: 224 Number of extensions: 15 Number of successful extensions: 6 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: 272 Length of database: 294 Length adjustment: 26 Effective length of query: 246 Effective length of database: 268 Effective search space: 65928 Effective search space used: 65928 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: 47 (22.7 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