Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate BPHYT_RS20780 BPHYT_RS20780 acyl-CoA dehydrogenase
Query= SwissProt::Q2LQN9 (414 letters) >FitnessBrowser__BFirm:BPHYT_RS20780 Length = 381 Score = 270 bits (691), Expect = 4e-77 Identities = 153/378 (40%), Positives = 228/378 (60%), Gaps = 6/378 (1%) Query: 36 ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95 +L++ + + E R A I P E+D + FP +LGL VP +GG G Sbjct: 2 KLSDTHQQIRETTRRFAQEVIRPITEELDRDERFPAEIYTQMGELGLFGITVPEAFGGAG 61 Query: 96 MDITTFAMVLEEIGKVCASTALM--LLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMT 153 +D+T +A+V+EE+ + AS A LL +LS+ G+ + + KY+ ++ L Sbjct: 62 LDVTAYALVMEELSRGYASVADQCGLLELVGTLLSV--HGTDSQRAKYMQPL-LRAKLRP 118 Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213 A+ TE AG+D+ ++T A++ D + ++G K +I N VAD+ V A TDP+ G +GM Sbjct: 119 AYCITEADAGTDVSGIRTTAMRTPDGWELSGAKLWIHNAPVADVAFVLARTDPAAGRRGM 178 Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273 S F+V+ G+ G E KMG R EL F+ +++P + L+G+EG+GF +M L Sbjct: 179 SIFIVDCALAGVSKGAKEHKMGQRASQVGELHFDRVKLPQDALLGQEGRGFHIMMSVLDK 238 Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333 RV A+ AVGIAQ LE A+ + + R+QFG IA IQ+M+ADMAT+++AARLLV Sbjct: 239 GRVGIAALAVGIAQAGLEAALDYAQTRKQFGSHIAEFQGIQWMLADMATDIQAARLLVHD 298 Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393 A L+A +R + MAK FA DTA+K + +AVQ+ GGSGY++ Y+VER+ R+AK+TQ Sbjct: 299 AAERLEA-GERASIACSMAKCFAGDTAVKHSANAVQIFGGSGYIRGYEVERLYRDAKITQ 357 Query: 394 IYTGTNQITRMVTGRSLL 411 IY GTNQI R + R L+ Sbjct: 358 IYEGTNQIQRTIVARDLI 375 Lambda K H 0.318 0.133 0.375 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: 329 Number of extensions: 15 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: 414 Length of database: 381 Length adjustment: 31 Effective length of query: 383 Effective length of database: 350 Effective search space: 134050 Effective search space used: 134050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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