Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_009779945.1 MED217_RS07745 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000152985.1:WP_009779945.1 Length = 602 Score = 180 bits (457), Expect = 8e-50 Identities = 119/391 (30%), Positives = 195/391 (49%), Gaps = 29/391 (7%) Query: 6 EEQKLTLDMVRDVATREIAPRALELDEK--SLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 EEQK+ + V++ REI P + K +L E R +LGLL +P Y G M Sbjct: 34 EEQKMMKETVKEFVDREIVPNKERFEHKDYALTEEVMRKA-GELGLLGIAVPDEYDGLGM 92 Query: 64 GVLTLALILEELGRVCASTALLLIAQTD-GMLPIIHGGSPELKERYLRRFAGESTLLTAL 122 G ++ L+ + + S A A T G +PI G+ E K++Y+ + A A Sbjct: 93 GFVSTMLVCDYISGATGSIATAFGAHTGIGTMPITLYGTEEQKKKYVPKLA-TGEWFGAY 151 Query: 123 AATEPAAGSDLLAMKTRAVRQGD--KYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGI 180 TEP AGSD + KT+A D Y INGQK +I+N ++ +V+A + +K I Sbjct: 152 CLTEPGAGSDANSGKTKAELSADGKSYKINGQKMWISNAGFCNLFIVFARIEDDKN---I 208 Query: 181 SAFVVEKGTP-GLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLS 239 + F+VE + G+ G E K+G+ S ++FF + VP EN++ G GF M L+ Sbjct: 209 TGFIVENDSSNGISLGEEEKKLGIHSSSTRQVFFNDTVVPVENMLAGRGEGFKIAMNALN 268 Query: 240 TNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTR 299 R+ AA + + +D+ V++ +RVQF PIA +++ +A+MAT + Sbjct: 269 VGRIKLAAACLDAQRRIIDMGVKYANERVQFKTPIAQFGAIKYKLAEMATNAYVCESASY 328 Query: 300 KAAELLDD------------------GDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGS 341 +AA+ ++D G ++ + S+ K AS+ + +Q+ GG Sbjct: 329 RAAKNIEDRIAIRMADGNSHQEAELKGVEEYAIECSILKVAASEDMQNCADEGIQIYGGM 388 Query: 342 GYMKENGVERMMRDAKLTQIYTGTNQITRMV 372 G+ + +E RDA++++IY GTN+I RM+ Sbjct: 389 GFSADAPMEAAWRDARISRIYEGTNEINRML 419 Lambda K H 0.319 0.134 0.371 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: 468 Number of extensions: 26 Number of successful extensions: 5 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: 380 Length of database: 602 Length adjustment: 34 Effective length of query: 346 Effective length of database: 568 Effective search space: 196528 Effective search space used: 196528 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 (21.7 bits) S2: 51 (24.3 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