Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate GFF2392 Psest_2440 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__psRCH2:GFF2392 Length = 383 Score = 266 bits (680), Expect = 7e-76 Identities = 156/381 (40%), Positives = 227/381 (59%), Gaps = 5/381 (1%) Query: 2 DHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGG 61 D L+ + +R +FA +AP + + +V +MG +GL G+ PEE+GG Sbjct: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62 Query: 62 MGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILG 121 DY+A +A+EE++ D + + S+G P+ +G+ AQK EWL L SG +G Sbjct: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 Query: 122 AFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPD 181 F LTEP GS+A RT A L + WV+NG+K F +N+ + L V AVT + Sbjct: 123 CFALTEPQAGSEAHNLRTRAELVDG--HWVLNGSKQFCSNAKR--SKLAIVFAVTDPEL- 177 Query: 182 GKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFL 241 GK +S+ +VP+ TPGF V K+G ASDT +S +D R+P ANLLGE+G+G A L Sbjct: 178 GKKGLSAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIAL 237 Query: 242 RILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMAR 301 L+ GRI I A A G+A+ + ++ YA ER FG+ I +Q+I +ADM+ + + AR Sbjct: 238 SNLEGGRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAAR 297 Query: 302 VGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDS 361 + AA AG P EA+ AKL++S +A +A QIHGGYG++ +YPV R +RD+ Sbjct: 298 LLILHAARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDA 357 Query: 362 KILEIGEGTSEVQRMLIAREL 382 +I +I EG+SE+QR+LIAREL Sbjct: 358 RITQIYEGSSEIQRLLIAREL 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: 386 Number of extensions: 14 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