Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_073038417.1 BUB04_RS07700 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF1051 (387 letters) >NCBI__GCF_900129305.1:WP_073038417.1 Length = 393 Score = 389 bits (1000), Expect = e-113 Identities = 196/387 (50%), Positives = 267/387 (68%), Gaps = 6/387 (1%) Query: 6 LNFALGETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYG 65 ++F L E M++E V + E+ P E ID+E+ FP D ++K E+G+LG+T+ E+YG Sbjct: 1 MDFQLSEEQRMMKEMVYKWSVNELGPLQEKIDEEDWFPPDFFKKCAEIGILGITIDEKYG 60 Query: 66 GAGLGYLAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHV 125 G G L +A+EE+SR +A++Y AHSNLC+N I++N N K +YLP +++GE + Sbjct: 61 GLGGDVLMQTLAVEEMSRICPGLAMTYAAHSNLCMNNIHKNANEFLKEKYLPAMVAGEKI 120 Query: 126 GALAMSEPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHG 185 GAL ++EPNAGSD +S++ RAE++GD+Y+LNG+K +ITNGP A+ ++YAKT +KGA G Sbjct: 121 GALGLTEPNAGSDAMSLRTRAERKGDKYILNGTKMFITNGPIADVILVYAKTAPEKGAKG 180 Query: 186 ITAFIVERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLD 245 I+AFIVE+D+ GFS K K GMRGS T EL F+D EVP EN++G EN GV V+ SGLD Sbjct: 181 ISAFIVEKDFPGFSVSRKLKKCGMRGSPTGELVFEDCEVPAENLVGEENMGVHVMTSGLD 240 Query: 246 YERVVLAGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLY 305 ER+VLAGG G+ Q LD V Y +R+QFGQ IG FQ IQ K+ADMY + A+R +Y Sbjct: 241 IERIVLAGGSVGMAQQALDYSVRYAAEREQFGQPIGNFQMIQQKLADMYARTEAARLMVY 300 Query: 306 AVAQACD------RGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLR 359 A+ +G K AA +L+ +E AT + QAIQI GG GY EFP +L R Sbjct: 301 RAAELAQKAPRGGKGTELTKQAAAAVLFASETATWVCNQAIQIHGGYGYCLEFPVQKLWR 360 Query: 360 DAKLYEIGAGTSEIRRMLIGRELFNES 386 DAKLYEIGAGT+EIRR+++ REL E+ Sbjct: 361 DAKLYEIGAGTNEIRRIIVARELLREA 387 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: 438 Number of extensions: 18 Number of successful extensions: 2 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: 393 Length adjustment: 31 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 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