Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000009985.1:WP_011385957.1 Length = 378 Score = 270 bits (691), Expect = 4e-77 Identities = 151/377 (40%), Positives = 228/377 (60%), Gaps = 5/377 (1%) Query: 6 TPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGD 65 T E + +R FA + +AP + H FP + + EMG +G G+ P E+ G G D Sbjct: 4 TEEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTD 63 Query: 66 YLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGL 125 Y++ +A+ E+A ++ + S+G MPI +GT+AQK E+L + GE LG F L Sbjct: 64 YVSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCL 123 Query: 126 TEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPL 185 TEP+ GSDA + RT AR D + +V++G K FI+ T G V + GK Sbjct: 124 TEPEAGSDAASIRTRARRDG--DHYVLSGAKQFIS---TAKNGQVAIVFAVTDPQAGKRG 178 Query: 186 ISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILD 245 IS+ +VP+ TPGFTV K+G + SDT +L+F D+RVPA+ LGE+G G L L+ Sbjct: 179 ISAFVVPTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLE 238 Query: 246 EGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWR 305 GR+ I+A + G+A+ +D ++ YA ER FG+ I +QA+ F++ADM + +A Sbjct: 239 GGRLGIAAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVL 298 Query: 306 DAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILE 365 AAS AG P KEA++AKL++S +A +A QIHGGYG++ ++PV R++RD ++ + Sbjct: 299 HAASLRDAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQ 358 Query: 366 IGEGTSEVQRMLIAREL 382 I EGTS++QR++I+R L Sbjct: 359 IYEGTSDIQRLVISRAL 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: 355 Number of extensions: 17 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 386 Length of database: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 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