Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_034273245.1 AMYHA_RS19255 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000504245.1:WP_034273245.1 Length = 386 Score = 516 bits (1330), Expect = e-151 Identities = 269/385 (69%), Positives = 303/385 (78%), Gaps = 3/385 (0%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 +D RL E + LR TV +FA V+P IGD+YER EFPY +V MG+MGLFGLPFPEE G Sbjct: 2 IDLRLDDEHDALRATVADFARSEVSPVIGDYYERGEFPYPLVATMGKMGLFGLPFPEELG 61 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 GMGGDYLAL IALEELARVDSSVAI L AGVSLGAMP++ FGT Q+ WLP LC GE L Sbjct: 62 GMGGDYLALCIALEELARVDSSVAIALSAGVSLGAMPLYRFGTVEQRERWLPSLCRGEAL 121 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 AFGLTEPDGG+DAGATRT A LD +WVINGTKCFITNSGTDIT +VTVTAVTG Sbjct: 122 AAFGLTEPDGGTDAGATRTRAELDGG--DWVINGTKCFITNSGTDITSVVTVTAVTGGHA 179 Query: 181 DGKPL-ISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQ 239 IS+I+VPSGTPGF V YSKVGW ASDT ELSF D RVP +NLLG++GRG AQ Sbjct: 180 GTSGAEISTILVPSGTPGFDVGPSYSKVGWCASDTHELSFTDCRVPESNLLGQRGRGMAQ 239 Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299 FL ILDE RIAISA+ GLAQGCVDE V+YA +R AFG IG+ QAIQF IADM + H Sbjct: 240 FLSILDESRIAISAVGVGLAQGCVDECVRYASQREAFGAPIGSRQAIQFTIADMATRVHT 299 Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 AR+ + A ++L+ GEPFK+EAA+AKL SS A+DNAR+ATQI GGYGFMNE PV R +R Sbjct: 300 ARLAYYAAVAKLLRGEPFKQEAAMAKLVSSNAAMDNARDATQIFGGYGFMNESPVGRFYR 359 Query: 360 DSKILEIGEGTSEVQRMLIARELGL 384 D+KILEIGEGTSEVQRMLIAR LGL Sbjct: 360 DAKILEIGEGTSEVQRMLIARHLGL 384 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: 538 Number of extensions: 16 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: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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