Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase
Query= BRENDA::P26440 (426 letters) >NCBI__GCF_000192475.1:WP_010441027.1 Length = 385 Score = 236 bits (603), Expect = 7e-67 Identities = 138/381 (36%), Positives = 216/381 (56%), Gaps = 10/381 (2%) Query: 45 LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGS 104 +++E R + +F+ + L P ++ R+FW Q G G++ + +YGG Sbjct: 11 VTDEHRMFAEMAGRFMDDALVPNTEKWAEDGVVD--RDFWLQAGQTGLMAGSIAEEYGGV 68 Query: 105 GLGY-LEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIG 163 G G + V + E+ +R G G YG S + + + G+E QK K+LPKL SGE IG Sbjct: 69 GGGMGFDSVTLYEQTAR--GDAGWGYGIQS-IVTHYITTYGSEDQKHKWLPKLASGEMIG 125 Query: 164 ALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASR 223 ALAM+EP GSDV ++K AEK GN Y L G+K +ITNG AD++IV AKTD + ++ Sbjct: 126 ALAMTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSL--GAK 183 Query: 224 GITAFIVE-KGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILG-HENKGVYVLMS 281 G++ VE +G GF + L+KLGM+G++T EL FED K+P N+LG E +G Y LM Sbjct: 184 GVSLIAVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMK 243 Query: 282 GLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQ 341 L ERL + LG + + T+ Y+ R+AFGQ++ FQ + K+A+ T+ R Sbjct: 244 QLPWERLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRS 303 Query: 342 YVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDAK 401 +V + + G A + V + +E ++ + +Q FGG G++ ++P+ R DA+ Sbjct: 304 FVNDCIGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADAR 363 Query: 402 LYEIGAGTSEVRRLVIGRAFN 422 + I GT+EV + +I R+ + Sbjct: 364 VQMIYGGTNEVMKELIARSLD 384 Lambda K H 0.321 0.137 0.410 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: 392 Number of extensions: 22 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: 426 Length of database: 385 Length adjustment: 31 Effective length of query: 395 Effective length of database: 354 Effective search space: 139830 Effective search space used: 139830 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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