Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= BRENDA::O87873 (258 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 116 bits (291), Expect = 4e-31 Identities = 83/257 (32%), Positives = 124/257 (48%), Gaps = 17/257 (6%) Query: 14 RDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDEH 73 RDG++L + + RPKAN +D A AM + P LR ++ G F F A D Sbjct: 9 RDGAVLEVVIDRPKANAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKF-FCAGWDLK 67 Query: 74 MPDQCAQMLKSLHGL-----VREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAK 128 + +G+ ++E+ D P++ A+ G C GGGLE+A + +L+ AA A Sbjct: 68 AAAS-GDAVDGDYGVGGFGGLQELRDLNKPVICAVNGLCCGGGLEIALSTDLIIAAEHAT 126 Query: 129 FGQPEIRLGVFAPAASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAA 188 F PEIR G A AAS LP R+ A D+L +GR +D E HR G ++ + Sbjct: 127 FALPEIRSGTVADAASIKLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEVVPAERLME 186 Query: 189 LRWFDEHIARLSAS-------SLRFAVRAARCDSVPRIKQKLDTVEALYLEELMASHDAV 241 W +ARL S +++ VR A + K+ + ++ L +S D + Sbjct: 187 RAW---ELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYSSEDQL 243 Query: 242 EGLKAFLEKRSANWENR 258 EG +AF EKRS W+ R Sbjct: 244 EGARAFAEKRSPIWKGR 260 Lambda K H 0.321 0.135 0.402 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: 158 Number of extensions: 6 Number of successful extensions: 3 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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 (21.9 bits) S2: 47 (22.7 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