Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate BPHYT_RS28040 BPHYT_RS28040 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS28040 Length = 377 Score = 276 bits (707), Expect = 5e-79 Identities = 165/383 (43%), Positives = 226/383 (59%), Gaps = 7/383 (1%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYG 60 MD T E +R +FA + +AP G + + P E+VR+MG +G G+ P E+G Sbjct: 1 MDSFYTDEQRMIRDAARDFATEQLAPHAGQWDREAQLPAEVVRQMGELGFLGMIVPAEWG 60 Query: 61 GMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEIL 120 G DY+A +ALEE+A ++ A + S+G PI FGT+AQK +L L +G + Sbjct: 61 GSYTDYVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGTEAQKDRYLQDLATGRRI 120 Query: 121 GAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKP 180 GAF LTEP GS+A RT A L + +W++NG+K F+TN L V AVT P Sbjct: 121 GAFCLTEPQAGSEANNLRTRAVLRDG--KWILNGSKQFVTNGSR--ADLAIVFAVTD--P 174 Query: 181 D-GKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQ 239 D GK +++ IVP+ TPGF V P K+G ASDT +S D VP ANLLGE G G Sbjct: 175 DRGKRGLTAFIVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPEANLLGEPGEGLRI 234 Query: 240 FLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHM 299 L L+ GRI I+A A G+A+ D + YA ER FG+ + +Q I +ADM + + Sbjct: 235 ALSNLEGGRIGIAAQAVGIARAAFDAARLYANERIQFGKALKEHQTIANMLADMATRLNA 294 Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 AR+ AA AG+P EA+ AKL++S +A + A QIHGGYG++ +Y V R +R Sbjct: 295 ARLLVHHAARLRTAGKPCLSEASQAKLFASELAEEICSNAIQIHGGYGYLEDYAVERHYR 354 Query: 360 DSKILEIGEGTSEVQRMLIAREL 382 D++I +I EGTSEVQRMLIAR + Sbjct: 355 DARITQIYEGTSEVQRMLIARHV 377 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: 374 Number of extensions: 13 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