Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase
Query= BRENDA::P26440 (426 letters) >NCBI__GCF_000428045.1:WP_029134232.1 Length = 397 Score = 199 bits (506), Expect = 1e-55 Identities = 126/376 (33%), Positives = 192/376 (51%), Gaps = 10/376 (2%) Query: 45 LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQLGNLGVLGITAPVQYGGS 104 L+EE+R +R T K+ QE L P+ E +R F RE ++G LG+LG+T Y + Sbjct: 23 LTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFD--REIMNEMGELGLLGVTID-GYDCA 79 Query: 105 GLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYIGA 164 GL Y+ + L+ E+ R + S+L ++ + G E Q+EKYLPKL +GE +G Sbjct: 80 GLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVGC 139 Query: 165 LAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRG 224 ++EP+ GSD MK +A Y L+G+K WITN P ADV IV+AK D Sbjct: 140 FGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDDEGV------ 193 Query: 225 ITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSGLD 284 I FI+EKGM G S K K +R S T E++ ++ +PA N+L + KG+ L+ Sbjct: 194 IRGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLLPNV-KGLAGPFGCLN 252 Query: 285 LERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACRQYVY 344 R +A G LG + + Y R+ FG+ + QL+Q K+A+M T + Q Sbjct: 253 RARYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCL 312 Query: 345 NVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDAKLYE 404 + + D G + + + +A A +A GGNG ++F + R + + Sbjct: 313 QLGRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVN 372 Query: 405 IGAGTSEVRRLVIGRA 420 GT +V L++GRA Sbjct: 373 TYEGTHDVHALILGRA 388 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: 407 Number of extensions: 26 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: 397 Length adjustment: 31 Effective length of query: 395 Effective length of database: 366 Effective search space: 144570 Effective search space used: 144570 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 Apr 09 2024. 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