Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF2397 Psest_2445 Acyl-CoA dehydrogenases
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__psRCH2:GFF2397 Length = 379 Score = 248 bits (633), Expect = 2e-70 Identities = 145/374 (38%), Positives = 209/374 (55%), Gaps = 5/374 (1%) Query: 39 EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98 E+Q + EM R A + P A + H +P A A LG LVP ++GG+ Sbjct: 5 EDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGY 64 Query: 99 TTFAMVLEEI--GKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 +AM LEEI G ST +M + + G + I+ G+ K +L + + AFA Sbjct: 65 LAYAMALEEIAAGDGACST-IMSVHNSVGCVPILRFGNEQQKSDFLTPLA-RGEQIGAFA 122 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216 TEP AGSD +++TRA + GD YV+NG K FIT+G A + V+A TDP G G+S F Sbjct: 123 LTEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGISAF 182 Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276 +V +PG E K+G ++ FEDL VP N +GEEG+G+ + L R+ Sbjct: 183 IVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRI 242 Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336 A+QAVG+A+ A E A + R+RE FGKPI + F +ADMAT++ AR +V A Sbjct: 243 GIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAA 302 Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396 L + + + MAK FAS+ A KV + A+Q +GG GY+ ++ VER+ R+ ++ QIY Sbjct: 303 LREV-GRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYE 361 Query: 397 GTNQITRMVTGRSL 410 GT+ I R+V R+L Sbjct: 362 GTSDIQRLVISRNL 375 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: 358 Number of extensions: 18 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 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