Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_034270170.1 AMYHA_RS09585 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000504245.1:WP_034270170.1 Length = 383 Score = 563 bits (1451), Expect = e-165 Identities = 288/384 (75%), Positives = 322/384 (83%), Gaps = 2/384 (0%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 +D RL E LR+TVE FA VAP IGDFYER EFPY IV +MG MGLFGLPFPE+Y Sbjct: 2 IDLRLDDTYETLRKTVENFAQREVAPVIGDFYEREEFPYGIVAQMGEMGLFGLPFPEKYD 61 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 GMGGDY AL +ALEELARVDSSVAITLEAGVSLGAMPI+ FGTD QK +WLP +C GE L Sbjct: 62 GMGGDYFALCLALEELARVDSSVAITLEAGVSLGAMPIYRFGTDEQKEQWLPAMCRGETL 121 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 GAFGLTEP GGSDAGAT+TTA++D + WVING+K FITNSGTDIT LVTVTAVTG K Sbjct: 122 GAFGLTEPGGGSDAGATKTTAKIDGDS--WVINGSKSFITNSGTDITSLVTVTAVTGTKD 179 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 +G IS+IIVPSGTPGFTV YSKVGWNASDT LSF DVRVP NL+G+QGRGYAQF Sbjct: 180 NGGKEISAIIVPSGTPGFTVEKKYSKVGWNASDTHGLSFDDVRVPQENLVGQQGRGYAQF 239 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L ILDEGRIAI+AL+TGLAQGCVDE ++YA ER AFGR IGA QAIQFK+ADME++ H A Sbjct: 240 LSILDEGRIAIAALSTGLAQGCVDECLRYAREREAFGRPIGANQAIQFKLADMELRTHNA 299 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R+ + AAS+++ GEPFKKEAAIAKL SS A+DNAREATQI GGYGFMNE+PV R +RD Sbjct: 300 RLAYYAAASKMLRGEPFKKEAAIAKLTSSNAAMDNAREATQIFGGYGFMNEFPVGRFYRD 359 Query: 361 SKILEIGEGTSEVQRMLIARELGL 384 +KILE+GEGTSEVQRMLIARELGL Sbjct: 360 AKILEVGEGTSEVQRMLIARELGL 383 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: 565 Number of extensions: 16 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: 383 Length adjustment: 30 Effective length of query: 356 Effective length of database: 353 Effective search space: 125668 Effective search space used: 125668 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