Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate BPHYT_RS23260 BPHYT_RS23260 isovaleryl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >FitnessBrowser__BFirm:BPHYT_RS23260 Length = 393 Score = 241 bits (615), Expect = 3e-68 Identities = 149/383 (38%), Positives = 220/383 (57%), Gaps = 10/383 (2%) Query: 5 LTPELEELRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGG 64 L E+E LR ++ FA +AP+ + +FP ++ R+ G +G+ G+ EEYGG Sbjct: 11 LGEEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTVSEEYGGANM 70 Query: 65 DYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFG 124 Y A IA+EE++R +SV ++ A +L IH GT+AQK ++LP+L SGE +GA Sbjct: 71 GYTAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVSGEHVGALA 130 Query: 125 LTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKP 184 ++EP+ GSD + + R ++ + +V+NGTK +ITN G D LV V A T + + + Sbjct: 131 MSEPNAGSDVVSMK--LRAEKKGDHYVLNGTKMWITN-GPDCDTLV-VYAKTDPEANSRG 186 Query: 185 LISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRIL 244 I++ IV G GF+VA K+G S T EL F DV VP N+LG+ G + L Sbjct: 187 -ITAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGAKVLMSGL 245 Query: 245 DEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADM-----EMKAHM 299 D R ++ TG+ +D V Y +R FG++IG +Q IQ K+AD+ +A++ Sbjct: 246 DYERAVLAGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQACRAYL 305 Query: 300 ARVGWRDAASRLVAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWR 359 VG + +K+ A LY++ A A EA QI GG G++NEYPV R+WR Sbjct: 306 YAVGRQLDTLGKEHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVGRLWR 365 Query: 360 DSKILEIGEGTSEVQRMLIAREL 382 D+K+ EIG GTSE++RMLI REL Sbjct: 366 DAKLYEIGAGTSEIRRMLIGREL 388 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: 418 Number of extensions: 31 Number of successful extensions: 4 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: 393 Length adjustment: 30 Effective length of query: 356 Effective length of database: 363 Effective search space: 129228 Effective search space used: 129228 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