Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011654331.1 RL_RS28910 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000009265.1:WP_011654331.1 Length = 375 Score = 270 bits (691), Expect = 4e-77 Identities = 159/374 (42%), Positives = 228/374 (60%), Gaps = 7/374 (1%) Query: 10 EELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYLAL 69 +++ +FA D +AP H FP E ++EMG +GL G+ PE YGG +A Sbjct: 8 QQISDLARDFARDRLAPGAAKRDREHLFPREELKEMGELGLLGMLVPEAYGGSDTGVVAY 67 Query: 70 GIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTEPD 129 ALEE+A D + + S+G +PI FGT+ Q+ +LP+L SGE +G F LTEP Sbjct: 68 AAALEEIAAGDGPCSTIMSVHSSVGCVPILKFGTEEQRQRFLPKLASGEWIGGFALTEPQ 127 Query: 130 GGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD-GKPLISS 188 GSDA +T AR D + +V++G+K FIT+ ++ V AVT PD GK I++ Sbjct: 128 AGSDASNLKTRARRDG--DYYVLDGSKQFITSGKNG--DVIIVFAVTD--PDVGKKGITA 181 Query: 189 IIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEGR 248 IVP+ TPG+ V K+G ++SDT +++F +R+PA LG +G GY L L+ GR Sbjct: 182 FIVPTDTPGYEVIRVEEKLGLHSSDTCQIAFNSMRIPAELRLGAEGEGYRIALANLEGGR 241 Query: 249 IAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDAA 308 I I+A A G+A+ + + YA ER AFG+ I +QA+ F++ADM ++ AR AA Sbjct: 242 IGIAAQAVGMARAAFEAARDYARERIAFGKPIVEHQAVAFRLADMAVRIEAARQLVFHAA 301 Query: 309 SRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIGE 368 S AG P EA++AKL++S +A +A QIHGGYG+M +YPV R++RD +I +I E Sbjct: 302 SLREAGLPCLSEASMAKLFASEMAERVCSDAIQIHGGYGYMADYPVERIYRDVRICQIYE 361 Query: 369 GTSEVQRMLIAREL 382 GTS+VQRM+IAR L Sbjct: 362 GTSDVQRMVIARNL 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: 411 Number of extensions: 22 Number of successful extensions: 2 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: 375 Length adjustment: 30 Effective length of query: 356 Effective length of database: 345 Effective search space: 122820 Effective search space used: 122820 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