Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate AZOBR_RS22310 AZOBR_RS22310 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >FitnessBrowser__azobra:AZOBR_RS22310 Length = 390 Score = 251 bits (641), Expect = 2e-71 Identities = 155/376 (41%), Positives = 212/376 (56%), Gaps = 5/376 (1%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 L E + D VR A EIAPRA E+D + FP F LG+L YGG M Sbjct: 13 LGESADMLRDTVRSFAADEIAPRAAEIDRTNEFPNELWRKFGDLGVLGITAEEEYGGAGM 72 Query: 64 GVLTLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTA 121 G L + +EE+ R AS L A ++ + I G+ E K RYL + +GE + A Sbjct: 73 GYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIRKNGTAEQKTRYLPKLISGEH--IGA 130 Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181 LA +EP AGSD+++MK RA +QGD+YV+NG K +ITNG AD +VVYA TD G +GI+ Sbjct: 131 LAMSEPNAGSDVVSMKLRAEKQGDRYVLNGTKMWITNGPDADTLVVYAKTDVNAGPRGIT 190 Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241 AF++EK G + K+GMRGS EL FE+ EVP ENI+G G G LM L Sbjct: 191 AFLIEKSFKGFSVAQKLDKLGMRGSNTGELVFEDCEVPEENILGGVGRGVNVLMSGLDYE 250 Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301 R A +GI Q +D+ V + DR QFG+PI +Q +ADM T + A++ Sbjct: 251 RAVLAGGPLGIMQACMDVVVPYLHDRKQFGQPIGEFQLMQGKLADMYTIMNAAKAYVYAV 310 Query: 302 AELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQI 361 A+ D G+ A + A A++ A + +A+Q LGG+GY+ E R++RDAKL +I Sbjct: 311 AKACDRGE-TARKDAAGAILFAAEKATWMALEAIQTLGGNGYINEYPTGRLLRDAKLYEI 369 Query: 362 YTGTNQITRMVTGRAL 377 GT++I RM+ GR L Sbjct: 370 GAGTSEIRRMLIGREL 385 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: 330 Number of extensions: 13 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: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 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