Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_043918838.1 jaqu_RS10025 acyl-CoA dehydrogenase family protein
Query= SwissProt::Q2LQN9 (414 letters) >NCBI__GCF_000877395.1:WP_043918838.1 Length = 379 Score = 225 bits (573), Expect = 2e-63 Identities = 134/377 (35%), Positives = 205/377 (54%), Gaps = 6/377 (1%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 L+EE + + M R++ EIAP A + P A+LGL V E GGTG+ Sbjct: 5 LSEESRAIFNMARDVGQAEIAPHARAWEAAGDIPRDLWPKLAELGLAGLYVSEEAGGTGL 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMTA 154 +V E + C S A L M + ++D GS LK++ LP+ T ++ Sbjct: 65 TRLDATLVFEALSMACPSVASFL--SIHNMCARMIDAYGSDELKDRMLPKALTCETWLS- 121 Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214 + TEPG+GSD A+KTRA + + + + G K FI+ G +D V A + + G +G+S Sbjct: 122 YCLTEPGSGSDAAALKTRAERTNEGWRLTGTKAFISGGGYSDAYIVMARSGEA-GPRGIS 180 Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274 FVVE GT GL +G E KMG R P ++ +D VPA NL+GEEG GF Y M L Sbjct: 181 AFVVEDGTDGLSFGGLEDKMGWRSQPTRQVQLDDAPVPASNLLGEEGHGFRYAMAGLDGG 240 Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334 R+ A+ ++G AQ AL+ + + RER+ FG+ +A QF +A+M E+++AR +R+A Sbjct: 241 RLNIAACSLGAAQQALDLTLAYVRERKAFGQSLADFQNTQFRLAEMEIELQSARTFLRQA 300 Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394 LD MAK ++ +V +Q+ GG GY+ +Y +E++ R+ ++ QI Sbjct: 301 AWHLDQGTPEATKFCAMAKKMVTEAGSRVVDGCLQLHGGYGYLADYGIEKLSRDLRVHQI 360 Query: 395 YTGTNQITRMVTGRSLL 411 GTN+I R++ R++L Sbjct: 361 LEGTNEIMRLIVARNML 377 Lambda K H 0.318 0.133 0.375 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: 308 Number of extensions: 12 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: 414 Length of database: 379 Length adjustment: 31 Effective length of query: 383 Effective length of database: 348 Effective search space: 133284 Effective search space used: 133284 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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