Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_012852325.1 TCUR_RS09745 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000024385.1:WP_012852325.1 Length = 382 Score = 540 bits (1390), Expect = e-158 Identities = 278/385 (72%), Positives = 314/385 (81%), Gaps = 8/385 (2%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 +D LT E ELR +VE FA VAP IGD YER EFPY+IV +MG MGLFGLPFPEEYG Sbjct: 2 IDFTLTEEQRELRASVERFARQEVAPVIGDLYERGEFPYQIVAKMGEMGLFGLPFPEEYG 61 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 GMGGDY AL +ALEELARVDSSVAITLEA VSLGAMPI+ FGT+ QK WLP+LCSGE L Sbjct: 62 GMGGDYFALCLALEELARVDSSVAITLEAAVSLGAMPIYRFGTEEQKRRWLPQLCSGERL 121 Query: 121 GAFGLTEPDGGSDA-GATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRK 179 AFGLTEP GGSD G RTTARL++ WVING+K FITNSGTDIT TV A+TG + Sbjct: 122 AAFGLTEPGGGSDVPGGMRTTARLEDG--HWVINGSKAFITNSGTDITAFTTVAALTGER 179 Query: 180 PDGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQ 239 IS+I+VP+GTPGFTV YSKVGW ASDTRELSFADVRVP NL+GE+GRGYAQ Sbjct: 180 E-----ISTILVPNGTPGFTVGRKYSKVGWAASDTRELSFADVRVPQENLVGERGRGYAQ 234 Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299 FL+ILDEGRIAI+AL+ GLAQGCVDE ++Y +R AFGR IG YQAIQFKIADME + H Sbjct: 235 FLQILDEGRIAIAALSVGLAQGCVDECLRYVRQRQAFGRAIGEYQAIQFKIADMEARTHT 294 Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 AR+ + AA++++AGEPFKKEAAIAKL +S A+DNAREATQI GGYGFMNE+PV R +R Sbjct: 295 ARLAYYAAAAKMLAGEPFKKEAAIAKLTASNAAMDNAREATQIFGGYGFMNEFPVGRFYR 354 Query: 360 DSKILEIGEGTSEVQRMLIARELGL 384 D+KILEIGEGTSEVQRMLIAR LGL Sbjct: 355 DAKILEIGEGTSEVQRMLIARSLGL 379 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: 571 Number of extensions: 18 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: 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 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