Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043918838.1 jaqu_RS10025 acyl-CoA dehydrogenase family protein
Query= reanno::psRCH2:GFF1051 (387 letters) >NCBI__GCF_000877395.1:WP_043918838.1 Length = 379 Score = 226 bits (575), Expect = 1e-63 Identities = 133/379 (35%), Positives = 211/379 (55%), Gaps = 5/379 (1%) Query: 6 LNFALGETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYG 65 ++FAL E + + AEIAP A A + P D+W K E+GL G+ VSEE G Sbjct: 1 MDFALSEESRAIFNMARDVGQAEIAPHARAWEAAGDIPRDLWPKLAELGLAGLYVSEEAG 60 Query: 66 GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHV 125 G GL L + E +S SVA H N+C I+ G+ E K R LPK ++ E Sbjct: 61 GTGLTRLDATLVFEALSMACPSVASFLSIH-NMCARMIDAYGSDELKDRMLPKALTCETW 119 Query: 126 GALAMSEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHG 185 + ++EP +GSD ++K RAE+ + + L G+K +I+ G ++ Y++ A++ + G G Sbjct: 120 LSYCLTEPGSGSDAAALKTRAERTNEGWRLTGTKAFISGGGYSDAYIVMARSG-EAGPRG 178 Query: 186 ITAFIVERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLD 245 I+AF+VE G S G DK+G R T ++ DD VP N+LG E G + M+GLD Sbjct: 179 ISAFVVEDGTDGLSFGGLEDKMGWRSQPTRQVQLDDAPVPASNLLGEEGHGFRYAMAGLD 238 Query: 246 YERVVLAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLY 305 R+ +A G Q LD+ + Y+ +RK FGQS+ +FQ Q ++A+M +L ++R +L Sbjct: 239 GGRLNIAACSLGAAQQALDLTLAYVRERKAFGQSLADFQNTQFRLAEMEIELQSARTFLR 298 Query: 306 AVAQACDRG--ETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKL 363 A D+G E T+ A + T E +++ +Q+ GG GY+ ++ +L RD ++ Sbjct: 299 QAAWHLDQGTPEATKFCAMAKKMVT-EAGSRVVDGCLQLHGGYGYLADYGIEKLSRDLRV 357 Query: 364 YEIGAGTSEIRRMLIGREL 382 ++I GT+EI R+++ R + Sbjct: 358 HQILEGTNEIMRLIVARNM 376 Lambda K H 0.318 0.135 0.391 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: 346 Number of extensions: 18 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: 387 Length of database: 379 Length adjustment: 30 Effective length of query: 357 Effective length of database: 349 Effective search space: 124593 Effective search space used: 124593 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 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