Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_054255950.1 BN2503_RS07075 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_001298675.1:WP_054255950.1 Length = 376 Score = 189 bits (479), Expect = 1e-52 Identities = 114/372 (30%), Positives = 190/372 (51%), Gaps = 5/372 (1%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78 LT+++ MVRD+ F ++++ P + + + + ++G G +PEQYGG+GL Sbjct: 3 LTQDQTMVRDAVRDFVREQITPHAARWDKEHHFPRDVHQGLAQLGAYGICVPEQYGGAGL 62 Query: 79 NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138 +YV L+ E+ D G + +SV + V + +G+EAQKQ++L LA GE +G F Sbjct: 63 DYVTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGSEAQKQQWLAPLARGEMLGAFC 122 Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGF 194 LTEP+ GSD ++ T A + Y + G K +IT+ V +V A D + F Sbjct: 123 LTEPHVGSDASALRTTATREGDDYVINGVKQFITSGKNGHVAIVIAVTDKAAGKKGMSAF 182 Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARY 253 ++ G + K+G +S T +I DN +P N+ + G K + L R Sbjct: 183 LVPTSNPGYQVARLEEKLGQHSSDTAQINFDNCRIPAANLIGAEGEGYKIALSALEGGRI 242 Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313 GI+ ++G A A + A QY+ +R+ FG+P+ +Q + +LAD T++ A Q Sbjct: 243 GIAAQSVGMARAAFECALQYSKERESFGQPIFNHQAVGFRLADCATQLEAARQLIWHAAS 302 Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373 ++D G ++ ++ K + A + A LGG G+ ++F V R ++ V YEG Sbjct: 303 LRDAGQPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERFYRDVRVCQIYEG 362 Query: 374 THDVHALILGRA 385 T DV +I+ RA Sbjct: 363 TSDVQKIIIQRA 374 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: 335 Number of extensions: 10 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: 376 Length adjustment: 30 Effective length of query: 363 Effective length of database: 346 Effective search space: 125598 Effective search space used: 125598 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 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