Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase
Query= BRENDA::Q39QF5 (380 letters) >NCBI__GCF_000009985.1:WP_043745120.1 Length = 378 Score = 252 bits (643), Expect = 1e-71 Identities = 152/380 (40%), Positives = 210/380 (55%), Gaps = 14/380 (3%) Query: 4 LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63 LT +Q+ D A E+AP A DE+ +FPE A+LG + GG+ + Sbjct: 5 LTPDQEAFRQAAHDFAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVGGSAL 64 Query: 64 GVLTLALILEELGRVCASTALLLIAQTDGMLPIIHGGSPELKERYL------RRFAGEST 117 L ALI EEL C STA + I G E + R+L R+FA Sbjct: 65 SRLDAALIFEELAAACPSTAAYISIHNMAAWMIDSFGDQEQRRRFLPDLCSMRKFA---- 120 Query: 118 LLTALAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGS 177 + TEP AGSD +++T+A R GD YV+NG K FI+ G +DV VV T G Sbjct: 121 ---SYCLTEPNAGSDAASLRTKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTGAP-GP 176 Query: 178 KGISAFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQT 237 KGIS VVE GTPGL +G+ E K+G + + + FE+ VP N IGAEG GF M+ Sbjct: 177 KGISCLVVEAGTPGLSFGKQEKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKG 236 Query: 238 LSTNRVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLL 297 L R+ A ++G A+ L+ A+ +T R QFG+ I+ QF +ADMAT +EA+RL+ Sbjct: 237 LDGGRINIGACSLGGARACLEHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLM 296 Query: 298 TRKAAELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAK 357 +AA LD +A ++ +MAK MA+D VT A+Q+ GG GY+KE +ER RD + Sbjct: 297 IHRAAHSLDSKSPQATVHCAMAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLR 356 Query: 358 LTQIYTGTNQITRMVTGRAL 377 + QI G+N+I R++ GRAL Sbjct: 357 VHQILEGSNEIMRVIIGRAL 376 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: 305 Number of extensions: 9 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: 378 Length adjustment: 30 Effective length of query: 350 Effective length of database: 348 Effective search space: 121800 Effective search space used: 121800 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