Align isovaleryl-CoA dehydrogenase subunit (EC 1.3.8.4) (characterized)
to candidate WP_011841987.1 RSPH17029_RS14905 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-16063 (387 letters) >NCBI__GCF_000015985.1:WP_011841987.1 Length = 403 Score = 209 bits (532), Expect = 1e-58 Identities = 130/378 (34%), Positives = 197/378 (52%), Gaps = 5/378 (1%) Query: 6 LNFALGETIDMLRDQVRGFVAAELQPRAAQIDQDNQFPMDMWRKFGEMGLLGITVDEEYG 65 + L E MLRD R + L PR ++ Q ++R+ GEMGLLG TV EEYG Sbjct: 23 MELQLSEEERMLRDGARAYAQERLMPRVTAAYREEQTDPAIFREMGEMGLLGATVPEEYG 82 Query: 66 GSALGYLAHAVVMEEISRASASVALSYGAHSNLCVNQIKRNGNAEQKARYLPALVSGEHI 125 G Y+++ ++ EI R + S+L + I G+ +Q+ RYLP L GE I Sbjct: 83 GLGASYVSYGLIAREIERVDSGYRSMMSVQSSLVMYPIYAYGSEDQRRRYLPGLAKGELI 142 Query: 126 GALAMSEPNAGSDVVSMKLRADRVGDRFVLNGSKMWITNGPDAHTYVIYAKTDADKGAHG 185 G ++EP+AGSD MK A + + +VL+GSKMWI+N P A +V++AK++A G Sbjct: 143 GCFGLTEPDAGSDPAGMKTVARKTAEGYVLSGSKMWISNAPIADVFVVWAKSEAHGGK-- 200 Query: 186 ITAFIVERDWKGFSRGPKL-DKLGMRGSNTCELIFQDVEVPEENVLGAVNGGVKVLMSGL 244 I F++E+ KG S PK+ KL +R S T E++ + VEV EE +L V G+K L Sbjct: 201 IRGFVLEKGMKGLS-APKIGGKLSLRASITGEIVMEGVEVGEEALLPGVE-GLKGPFGCL 258 Query: 245 DYERVVLSGGPVGIMQACMDVVVPYIHDRRQFGQSIGEFQLVQGKVADMYTALNASRAYL 304 + R +S G +G +AC+ Y DRRQFG+ + + QL Q K+A+M T + Sbjct: 259 NRARYGISWGVLGAAEACLHAARQYGLDRRQFGRPLAQTQLYQLKLANMMTDIALGAQAS 318 Query: 305 YAVAAACDRGETTRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPTGRLLRDAKLY 364 V D + + V + +A + A A + GGNG EF R + + + Sbjct: 319 LRVGRLLDEANAAPEMISIVKRSNCGKALEAARHARDMHGGNGIQEEFHVMRHMANLETV 378 Query: 365 EIGAGTSEIRRMLIGREL 382 GT ++ +++GR + Sbjct: 379 NTYEGTHDVHALILGRAI 396 Lambda K H 0.319 0.136 0.395 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: 371 Number of extensions: 15 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: 403 Length adjustment: 31 Effective length of query: 356 Effective length of database: 372 Effective search space: 132432 Effective search space used: 132432 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 10 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