Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__Burk376:H281DRAFT_02091 Length = 378 Score = 280 bits (717), Expect = 4e-80 Identities = 154/372 (41%), Positives = 224/372 (60%), Gaps = 3/372 (0%) Query: 12 LRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYLALGI 71 +R + F + V P + FP ++ R++ +G +G+ PE YGG G D LAL + Sbjct: 10 VRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGAGMDALALAL 69 Query: 72 ALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTEPDGG 131 LEE+A D + + + +G DAQK EWL L GE+LGAF LTEP G Sbjct: 70 ILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGAFCLTEPQAG 129 Query: 132 SDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPLISSIIV 191 SDA A RTTA D+ + +V+NG K FIT+ G V + K GK IS+ IV Sbjct: 130 SDASALRTTATRDKDGDAYVLNGVKQFITSGKN---GDVAIVMAVTDKAAGKRGISAFIV 186 Query: 192 PSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEGRIAI 251 P+ + G+ VA K+G ++SDT ++ F D RVPAANL+G +G GY L L+ GRI I Sbjct: 187 PTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLEGGRIGI 246 Query: 252 SALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDAASRL 311 +A + G+A+ + ++ YA ER +FG+ + ++QA+QF++ADM + AR AAS Sbjct: 247 AAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIWHAASLK 306 Query: 312 VAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIGEGTS 371 AG+P EAA+AKL++S A A QIHGGYG+++++PV R++RD ++ +I EGTS Sbjct: 307 DAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQIYEGTS 366 Query: 372 EVQRMLIARELG 383 ++Q++LIAR LG Sbjct: 367 DIQKILIARGLG 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: 410 Number of extensions: 15 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: 378 Length adjustment: 30 Effective length of query: 356 Effective length of database: 348 Effective search space: 123888 Effective search space used: 123888 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