Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_058929103.1 AU252_RS00840 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_001484605.1:WP_058929103.1 Length = 382 Score = 528 bits (1361), Expect = e-155 Identities = 270/380 (71%), Positives = 307/380 (80%), Gaps = 2/380 (0%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 L+ + E+LRR+V++FA VVAP E H FPYE+V +M MGLFGLPFPEE+GGMGG Sbjct: 4 LSEDYEDLRRSVQDFAQTVVAPVSAKHDEAHSFPYEVVEQMAGMGLFGLPFPEEHGGMGG 63 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124 DY AL +ALEEL +VD SVAITLEAGV LGAMPI FGT+ QKAEWLP L +G L FG Sbjct: 64 DYFALALALEELGKVDQSVAITLEAGVGLGAMPIFRFGTEEQKAEWLPDLAAGRALAGFG 123 Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184 LTEP G+DAG T TTARL++ WVINGTK FITNSGTDIT LVTVTAVTG +GK Sbjct: 124 LTEPGAGTDAGGTATTARLEDGC--WVINGTKQFITNSGTDITSLVTVTAVTGVAENGKK 181 Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244 IS+IIVPSGT GF V Y+KVGWNASDT LSF DVRVP NLLGE+GRGYA FL IL Sbjct: 182 EISTIIVPSGTEGFVVQPAYNKVGWNASDTHPLSFTDVRVPEGNLLGERGRGYANFLSIL 241 Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGW 304 DEGRIAI+ALATG AQGCVDESVKYA ER AFG+NIG++QAI FKIA ME +AH+AR + Sbjct: 242 DEGRIAIAALATGAAQGCVDESVKYAKERAAFGQNIGSFQAISFKIARMEARAHVARAAY 301 Query: 305 RDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKIL 364 AA R+++G+PFKKEAAIAK+ S A+DNAR+ATQIHGGYGFMNEYPV+R +RDSKIL Sbjct: 302 YGAARRMLSGKPFKKEAAIAKMIGSEAAMDNARDATQIHGGYGFMNEYPVSRHYRDSKIL 361 Query: 365 EIGEGTSEVQRMLIARELGL 384 EIGEGT+EVQ MLIARELGL Sbjct: 362 EIGEGTTEVQLMLIARELGL 381 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: 541 Number of extensions: 15 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: 382 Length adjustment: 30 Effective length of query: 356 Effective length of database: 352 Effective search space: 125312 Effective search space used: 125312 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