Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_001298675.1:WP_054255950.1 Length = 376 Score = 263 bits (672), Expect = 6e-75 Identities = 148/382 (38%), Positives = 231/382 (60%), Gaps = 13/382 (3%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 LT + +R V +F + + P + + H FP ++ + + ++G +G+ PE+YGG G Sbjct: 3 LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHL----FGTDAQKAEWLPRLCSGEIL 120 DY+ L + LEE+A D + +S+ P++ +G++AQK +WL L GE+L Sbjct: 63 DYVTLALVLEEIAAGDGGTS----TAISVTNCPVNAILMRYGSEAQKQQWLAPLARGEML 118 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 GAF LTEP GSDA A RTTA + +++VING K FIT+ G V + K Sbjct: 119 GAFCLTEPHVGSDASALRTTATREG--DDYVINGVKQFITSGKN---GHVAIVIAVTDKA 173 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 GK +S+ +VP+ PG+ VA K+G ++SDT +++F + R+PAANL+G +G GY Sbjct: 174 AGKKGMSAFLVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIA 233 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L L+ GRI I+A + G+A+ + +++Y+ ER +FG+ I +QA+ F++AD + A Sbjct: 234 LSALEGGRIGIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAA 293 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R AAS AG+P KEAA+AKL++S +A A Q GGYG +N++PV R +RD Sbjct: 294 RQLIWHAASLRDAGQPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRD 353 Query: 361 SKILEIGEGTSEVQRMLIAREL 382 ++ +I EGTS+VQ+++I R L Sbjct: 354 VRVCQIYEGTSDVQKIIIQRAL 375 Lambda K H 0.318 0.136 0.402 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: 402 Number of extensions: 17 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: 386 Length of database: 376 Length adjustment: 30 Effective length of query: 356 Effective length of database: 346 Effective search space: 123176 Effective search space used: 123176 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 24 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