Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_041096890.1 SUTH_RS02660 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000828635.1:WP_041096890.1 Length = 379 Score = 293 bits (749), Expect = 7e-84 Identities = 160/378 (42%), Positives = 237/378 (62%), Gaps = 5/378 (1%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 LT E E++R + +FA + +APK ++ FP E +R +G +G+ G+ PE++GG G Sbjct: 3 LTSEQEQIRDMLRDFAREQLAPKAAEWDRTSHFPREELRALGELGVCGMVVPEQWGGAGL 62 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124 DY++L +ALEE+A D + + + S+ PI+ FGTDAQK ++L +L SGE LG F Sbjct: 63 DYVSLALALEEIAAGDGATSTIISVQNSVVCGPINAFGTDAQKEKYLKKLASGEWLGCFC 122 Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184 LTEP GSDA A RT A D + WV+NG K FIT +V G GK Sbjct: 123 LTEPHVGSDAAAIRTRAVRDG--DHWVLNGVKQFITTGKNAQVAVVFAVTDPGA---GKK 177 Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244 IS+ IVP+ PG+ VA K+G +ASDT ++ F + R+PA NLLG +G+GY L L Sbjct: 178 GISAFIVPADAPGYIVARVEEKLGQHASDTAQILFENCRIPAENLLGAEGQGYRIALSNL 237 Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGW 304 + GRI ISA A G+A+ + ++ Y+ ER +FG+ I +QA+ F++ADM + +AR Sbjct: 238 EGGRIGISAQAVGMARAAFEAALHYSHERQSFGKPIFEHQAVNFRLADMATQIEVARQMV 297 Query: 305 RDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKIL 364 AA+ AG P KEA++AKL++S +A +A QIHGGYG+++++PV R++RD ++ Sbjct: 298 HHAAALRDAGRPCLKEASMAKLFASEMAEKVCSDAIQIHGGYGYVSDFPVERIYRDVRVC 357 Query: 365 EIGEGTSEVQRMLIAREL 382 +I EG S++QR++I R L Sbjct: 358 QIYEGASDIQRLVIGRSL 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: 375 Number of extensions: 14 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: 386 Length of database: 379 Length adjustment: 30 Effective length of query: 356 Effective length of database: 349 Effective search space: 124244 Effective search space used: 124244 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 Apr 09 2024. 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