Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_011913066.1 PST_RS09725 acyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_000013785.1:WP_011913066.1 Length = 383 Score = 265 bits (678), Expect = 1e-75 Identities = 157/382 (41%), Positives = 227/382 (59%), Gaps = 7/382 (1%) Query: 2 DHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61 D L+ + +R +FA +AP + + +V +MG +GL G+ PEE+GG Sbjct: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDALVAQMGELGLLGMVVPEEWGG 62 Query: 62 MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121 DY+A +A+EE++ D + + S+G P+ +G+ AQK EWL L SG +G Sbjct: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLAELASGRAIG 122 Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD 181 F LTEP GS+A RT A L + +WV+NG+K F +N+ L V AVT PD Sbjct: 123 CFALTEPQAGSEAHNLRTRAELVDG--QWVLNGSKQFCSNAKR--AKLAIVFAVTD--PD 176 Query: 182 -GKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQF 240 GK +S+ +VP+ T GF V K+G ASDT +S +D R+P ANLLGE+G+G A Sbjct: 177 LGKKGLSAFLVPTDTAGFAVERSEHKMGIRASDTCAVSLSDCRIPQANLLGERGKGLAIA 236 Query: 241 LRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMA 300 L L+ GRI I A A G+A+ + ++ YA ER FG+ I +Q+I +ADM+ + + A Sbjct: 237 LSNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAA 296 Query: 301 RVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRD 360 R+ AA AG P EA+ AKL++S +A +A QIHGGYG++ +YPV R +RD Sbjct: 297 RLLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRD 356 Query: 361 SKILEIGEGTSEVQRMLIAREL 382 ++I +I EG+SE+QR+LIAREL Sbjct: 357 ARITQIYEGSSEIQRLLIAREL 378 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: 379 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: 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 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