Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_073037627.1 BUB04_RS05240 glutaryl-CoA dehydrogenase Acd
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_900129305.1:WP_073037627.1 Length = 385 Score = 216 bits (549), Expect = 1e-60 Identities = 128/379 (33%), Positives = 206/379 (54%), Gaps = 6/379 (1%) Query: 18 QLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSG 77 +LTEE+++V++ A +FA++++ P + E + + R+MGE+G G IPE+YGG+G Sbjct: 4 ELTEEQKIVQEQARRFAENEILPTLEEEEKGHVFNRERLRKMGELGFFGCAIPEEYGGNG 63 Query: 78 LNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCF 137 + +V L+ ++ ++ +R ++Q+ + +N+FGTE QK+ Y+P SGE +G F Sbjct: 64 MGFVESVLMTEQIAKVSPSWRVPFNMQNIGPAITVNQFGTEEQKRAYIPGWVSGEKVGFF 123 Query: 138 GLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GDIRG 193 +TEPN GSD M T A+ + + L G KMWI+N+PIADV +V+A D + Sbjct: 124 AITEPNAGSDVAGMRTTAKDMGDHWELNGQKMWISNAPIADVGLVYAYTDKEKKYKGMTC 183 Query: 194 FVLE-KGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLNSA 251 F+++ G + AI K+GL S TGEI+ D +P++ + V G K LN+ Sbjct: 184 FIVDVAGNPNIVTRAIESKLGLHCSPTGEIIFDGAKIPKDAVLGQVGDGFKICMWMLNNT 243 Query: 252 RYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRL 311 R + GALG + AC A +Y +R QFG+P++ Q+IQ ++A+M E A Sbjct: 244 RISCAAGALGVSGACLDLAVKYANERTQFGKPISTYQMIQAQIAEMAAEHEAAKWLVYHA 303 Query: 312 GRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTY 371 +KD+G TSI K + A+ A A + G G S E+ + R + + Sbjct: 304 AYLKDQGKPNQLQTSIAKYYASEAAVRAANEAMKIFGSYGFSTEYPIERFYRDAKSYQIV 363 Query: 372 EGTHDVHALILGRAQTGIQ 390 EGT +V +I+ G Q Sbjct: 364 EGTSNVQKMIIAGITCGHQ 382 Lambda K H 0.320 0.137 0.413 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: 359 Number of extensions: 16 Number of successful extensions: 3 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: 393 Length of database: 385 Length adjustment: 30 Effective length of query: 363 Effective length of database: 355 Effective search space: 128865 Effective search space used: 128865 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