Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate CCNA_02254 CCNA_02254 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__Caulo:CCNA_02254 Length = 386 Score = 242 bits (617), Expect = 1e-68 Identities = 151/374 (40%), Positives = 216/374 (57%), Gaps = 11/374 (2%) Query: 11 TLDMVRDVATR----EIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66 T D +R+ R +IAP A ++DE + FP LGL + +GG +G L Sbjct: 16 TADAIRETTARFAADKIAPIAAKIDETNSFPRELWVPMGDLGLHGITVEEEFGGLGLGYL 75 Query: 67 TLALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRF-AGESTLLTALAA 124 + +EE+ R AS L A ++ + I +PE K RYL + +GE + +LA Sbjct: 76 EHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWATPEQKARYLPKLISGEH--VGSLAM 133 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 +E AGSD+++MK RA + GD+Y++NG K +ITN AD +VVYA T +GS+GI+AF+ Sbjct: 134 SEAGAGSDVVSMKLRAEQVGDRYILNGTKFWITNAPHADTLVVYAKTG--EGSRGITAFI 191 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 VEKG G + KMGMRGS +EL FE+ E+P EN++G G G LM L R Sbjct: 192 VEKGMKGFSVSKKLDKMGMRGSDTAELVFEDCEIPEENVMGPVGGGVGVLMSGLDYERAV 251 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 AA +GI Q LD+ + + +DR QFG+PI +Q +ADM A+ ++R A+ Sbjct: 252 LAAGPLGIMQACLDVVLPYVRDRKQFGQPIGSFQLMQGKIADMYVALNSARAYVYAVAKA 311 Query: 305 LDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTG 364 D G K + A MAS+ A++V+ +A+Q LGG+GY KE VER++RDAKL I G Sbjct: 312 CDAG-KTTRFDAAGAILMASENAVKVSLEAIQALGGAGYTKEWPVERLLRDAKLYDIGAG 370 Query: 365 TNQITRMVTGRALL 378 TN+I R + GR L+ Sbjct: 371 TNEIRRFLIGRELI 384 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: 307 Number of extensions: 13 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 350 Effective length of database: 356 Effective search space: 124600 Effective search space used: 124600 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: 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