Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__Korea:Ga0059261_4052 Length = 385 Score = 234 bits (597), Expect = 3e-66 Identities = 149/383 (38%), Positives = 212/383 (55%), Gaps = 18/383 (4%) Query: 37 LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARD----LFADLGLLSPLVPVEYG 92 L+E +++ + + A I P A +ID FP RD +LGL V E+G Sbjct: 10 LSETAEMIRDTTQRFAKERIEPLAAKIDAEDWFP---RDELWTAMGELGLHGITVDEEFG 66 Query: 93 GTGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRF--GEKS 149 G G+ + EE+ + AS L A ++ ++ I SPA K KYLPR GE Sbjct: 67 GLGLGYLEHVIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEH- 125 Query: 150 TLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKG 209 + + A +E GAGSD+++MK RA KGD+YV+NG K +ITN + AD L V+A T +G Sbjct: 126 --VGSLAMSEAGAGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKT--GEG 181 Query: 210 AKGMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMG 269 ++G++TF++E+ PG G KMGMRG P +EL F+D EVP EN++G G LM Sbjct: 182 SRGITTFLIEKDMPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMS 241 Query: 270 ALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARL 329 L R A +GI Q L+ + + RER+QFG+ I +Q +ADM + +AR Sbjct: 242 GLDYERTVLAGIQLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARA 301 Query: 330 LVRKATTLLDA-KDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMRE 388 V DA K R G A AS+ A +V +AVQ +GG+GY +++ VER +R+ Sbjct: 302 YVYAVAQACDAGKTTRFDAAG--AILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRD 359 Query: 389 AKLTQIYTGTNQITRMVTGRSLL 411 AKL I GTN+I RM+ GR L+ Sbjct: 360 AKLLDIGAGTNEIRRMLIGRELI 382 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: 332 Number of extensions: 21 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: 414 Length of database: 385 Length adjustment: 31 Effective length of query: 383 Effective length of database: 354 Effective search space: 135582 Effective search space used: 135582 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