Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_012760746.1 RLEG_RS35160 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000023185.1:WP_012760746.1 Length = 381 Score = 252 bits (644), Expect = 1e-71 Identities = 154/374 (41%), Positives = 214/374 (57%), Gaps = 9/374 (2%) Query: 11 TLDMVRDVATR----EIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66 T D +R+ R IAP A+E+DE + FP LGL + +GG +G L Sbjct: 9 TADAIRETTARFAADHIAPLAVEIDESNTFPRQLWPEMGALGLHGITVEEEFGGAGLGYL 68 Query: 67 TLALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRF-AGESTLLTALAA 124 + +EE+ R AS L A ++ + I SPE K RYL + +GE + +LA Sbjct: 69 DHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRYLPKLISGEH--VGSLAM 126 Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184 +E AGSD+++M+ RA ++GD+YV+NG K +ITN ADV+VVYA TDP G KGISA + Sbjct: 127 SEVGAGSDVVSMRLRAEKKGDRYVLNGTKFWITNAPHADVLVVYAKTDPAAGPKGISALI 186 Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244 +EKG PG + SK+GMRGS +EL FE+ VPAE ++G EG G LM L R Sbjct: 187 IEKGLPGFGVSKKLSKLGMRGSDTAELVFEDCAVPAEALMGREGEGVKILMSGLDYERAV 246 Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304 A +GI Q LD+ + + +DR QFGK I +Q +ADM A+ ++R A Sbjct: 247 LAGGPLGIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYSVARA 306 Query: 305 LDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTG 364 D G + + A AS+ A++V+ +A+Q LGG+GY KE VER +RDAKL I G Sbjct: 307 CDAG-RATRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDIGAG 365 Query: 365 TNQITRMVTGRALL 378 TN+I R + GR L+ Sbjct: 366 TNEIRRYLIGRELI 379 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: 328 Number of extensions: 11 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: 380 Length of database: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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 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