Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__azobra:AZOBR_RS22300 Length = 377 Score = 286 bits (731), Expect = 9e-82 Identities = 161/379 (42%), Positives = 231/379 (60%), Gaps = 5/379 (1%) Query: 4 RLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMG 63 RLT E +R +FA + +AP + FP E + EMGR+GL G+ PEE+ G G Sbjct: 2 RLTEEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAG 61 Query: 64 GDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAF 123 D++A +A+EE+A D +++ + S+G MPI FG+ QK +L + GE LG F Sbjct: 62 TDHIAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQLGCF 121 Query: 124 GLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGK 183 LTEP GSDA A +T AR D N WV+NGTK FIT SG + V + GK Sbjct: 122 CLTEPQAGSDAAAIKTRARRDG--NHWVLNGTKQFIT-SGKNAD--VAIVFAVSDPEAGK 176 Query: 184 PLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRI 243 I++ +VP+ TPGF VA K+G + SDT ++ D R+PA +LG +G GY L Sbjct: 177 KGITAFVVPTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALAN 236 Query: 244 LDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVG 303 L+ GRI I++ + G+A+ +D + +YA ER + G I +QA+ F++ADM K AR Sbjct: 237 LEGGRIGIASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQL 296 Query: 304 WRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKI 363 AAS AGEP KEAA+AKL++S +A +A QIHGGYG++N++PV R++RD ++ Sbjct: 297 VLHAASLRDAGEPCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRV 356 Query: 364 LEIGEGTSEVQRMLIAREL 382 +I EGTS++QR++I+R L Sbjct: 357 CQIYEGTSDIQRLVISRAL 375 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: 387 Number of extensions: 9 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: 377 Length adjustment: 30 Effective length of query: 356 Effective length of database: 347 Effective search space: 123532 Effective search space used: 123532 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 17 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