Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_028316389.1 G491_RS0124250 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000429905.1:WP_028316389.1 Length = 382 Score = 339 bits (869), Expect = 9e-98 Identities = 181/383 (47%), Positives = 247/383 (64%), Gaps = 2/383 (0%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 MD L E E +R V FA +AP + E+ EF E+ + MG +GLFG+ PE YG Sbjct: 1 MDFDLNKEQEMIRDAVRSFAEKEIAPVALELDEKEEFSPELTKAMGEIGLFGMFVPEVYG 60 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G DY++ IA+EE+AR+D S A T+ AG SLG PI+ FG++ QK ++LP+LC+GE L Sbjct: 61 GQEMDYISYAIAVEEVARIDGSQAATVAAGNSLGIGPINYFGSEEQKKKYLPKLCTGEAL 120 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 FGLTEP+ GSDAG ++TTA D NEWV+NG+K FITN+ +++ VTV AVTG + Sbjct: 121 WGFGLTEPEAGSDAGGSKTTAVKD--GNEWVLNGSKIFITNAACELSLGVTVQAVTGTRA 178 Query: 181 DGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 DG+P + ++ GTPGFT A + K+ W +S T EL F +VR+ +LG+ G G+ Q Sbjct: 179 DGRPETTCFLLEHGTPGFTAKAMHKKLMWRSSSTAELYFDNVRLKEDAILGKPGDGFKQM 238 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L+ LD GR++I A+ G AQG + ++KYA +R FG+ I +QA FK+AD M+ A Sbjct: 239 LKTLDGGRLSIGAMGLGGAQGAYELALKYAKQRKQFGQPISKFQANAFKLADCAMEIECA 298 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R A PF+K A++AKLY S V A A QIHGGYG M EY V R +RD Sbjct: 299 RNLLYKACWLRSQHRPFQKLASMAKLYCSEVMYRVANHAVQIHGGYGLMKEYNVERFYRD 358 Query: 361 SKILEIGEGTSEVQRMLIARELG 383 K+L+IGEGTSE+QR++I+R +G Sbjct: 359 QKLLDIGEGTSEIQRLVISRYIG 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: 426 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: 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