Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_002893965.1:WP_050655857.1 Length = 380 Score = 246 bits (629), Expect = 6e-70 Identities = 138/382 (36%), Positives = 215/382 (56%), Gaps = 11/382 (2%) Query: 4 RLTP--ELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61 RL P E +L + A V+APK+ ++ + ++P + +G+ GL LP+PEE+GG Sbjct: 5 RLMPSQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGG 64 Query: 62 MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121 Y LEE+A ++VA+ + SL P+ FGTD QK WLP + G +G Sbjct: 65 GDQPYEVYLQVLEEIASRWAAVAVAVSVH-SLSCFPLFTFGTDEQKNRWLPDMLGGNTIG 123 Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSG-TDITGLVTVTAVTGRKP 180 A+ L+E GSDA A + + + + +NG+K +ITN G D L T+ Sbjct: 124 AYSLSEAQAGSDAAAL--SCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTS-----D 176 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 DG +S ++V G + P K+G A T ++ D +P L+G++G+G Sbjct: 177 DGSRGVSCLLVDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIA 236 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 LD GR+ I+A+A G+AQG +D++V YA ER AFG+ I +Q + F +ADM A Sbjct: 237 FSALDSGRLGIAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSA 296 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R + DAA R AG P+ + A++AKL ++ A+ +A Q+ GGYG+ ++PV R R+ Sbjct: 297 RATYLDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMRE 356 Query: 361 SKILEIGEGTSEVQRMLIAREL 382 +KI +I EGT+++QR++IAR+L Sbjct: 357 AKITQIFEGTNQIQRLVIARQL 378 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: 446 Number of extensions: 27 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: 380 Length adjustment: 30 Effective length of query: 356 Effective length of database: 350 Effective search space: 124600 Effective search space used: 124600 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