Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate GFF928 HP15_907 acyl-CoA dehydrogenase domain protein
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Marino:GFF928 Length = 388 Score = 270 bits (689), Expect = 7e-77 Identities = 149/376 (39%), Positives = 211/376 (56%), Gaps = 2/376 (0%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96 LTE+Q E R A + +AP A + D H FPV ++G + P GG G+ Sbjct: 5 LTEDQLAFREAARAFAEKSMAPHAAKWDNEHIFPVDMMKEAGEMGFMGMYTPEALGGMGL 64 Query: 97 DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156 ++++EE+ C STA + + S LK++ +P+ L ++ Sbjct: 65 SRLDTSVIVEELAAACPSTAAFITIHNMATWMVASFASDDLKQEIVPKLASGEWL-ASYC 123 Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTD-PSKGAKGMST 215 TEPGAGSD +++T+AV+ GD YVING K FI+ DIL + A T P G KG+ST Sbjct: 124 LTEPGAGSDAASLRTKAVRDGDSYVINGSKVFISGAGATDILVLMARTGAPDSGYKGIST 183 Query: 216 FVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINR 275 FV+ G+ YG NE+KMG P + E++ +PA N VG+EG GFA M L R Sbjct: 184 FVIPADADGISYGKNEEKMGWHSQPTRMISLENVRIPASNRVGDEGDGFAIAMKGLDGGR 243 Query: 276 VFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKAT 335 + A+ ++G AQ AL RA + EREQFGKP+A +QF +ADMAT + AAR +VR Sbjct: 244 LNIATCSLGGAQAALLRARNYMHEREQFGKPLAAFQALQFKLADMATNLVAARQMVRLGA 303 Query: 336 TLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY 395 LD D L MAK FA+D +V +A+Q+ GG GY++EY +ER +R+ ++ QI Sbjct: 304 FKLDNADPEATLHCAMAKRFATDACFEVVNEALQLHGGYGYIREYPLERYLRDLRVHQIL 363 Query: 396 TGTNQITRMVTGRSLL 411 GTN+I R++ R LL Sbjct: 364 EGTNEIMRLIVARRLL 379 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: 351 Number of extensions: 10 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: 388 Length adjustment: 31 Effective length of query: 383 Effective length of database: 357 Effective search space: 136731 Effective search space used: 136731 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 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