Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_041096890.1 SUTH_RS02660 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000828635.1:WP_041096890.1 Length = 379 Score = 234 bits (596), Expect = 4e-66 Identities = 138/375 (36%), Positives = 206/375 (54%), Gaps = 5/375 (1%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78 LT E+ +RD FA+++LAP+ E R R +GE+G+ G +PEQ+GG+GL Sbjct: 3 LTSEQEQIRDMLRDFAREQLAPKAAEWDRTSHFPREELRALGELGVCGMVVPEQWGGAGL 62 Query: 79 NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138 +YV L E+ D +++SVQ+S+V PIN FGT+AQK+KYL KLASGEW+GCF Sbjct: 63 DYVSLALALEEIAAGDGATSTIISVQNSVVCGPINAFGTDAQKEKYLKKLASGEWLGCFC 122 Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGF 194 LTEP+ GSD ++ TRA + + L G K +IT A V VV+A D G I F Sbjct: 123 LTEPHVGSDAAAIRTRAVRDGDHWVLNGVKQFITTGKNAQVAVVFAVTDPGAGKKGISAF 182 Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF-PDVRGLKGPFTCLNSARY 253 ++ G + K+G AS T +I+ +N +P EN+ + +G + + L R Sbjct: 183 IVPADAPGYIVARVEEKLGQHASDTAQILFENCRIPAENLLGAEGQGYRIALSNLEGGRI 242 Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313 GIS A+G A A + A Y+ +RQ FG+P+ +Q + +LADM T+I +A Q Sbjct: 243 GISAQAVGMARAAFEAALHYSHERQSFGKPIFEHQAVNFRLADMATQIEVARQMVHHAAA 302 Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373 ++D G ++ S+ K + A + A + GG G +F V R ++ V YEG Sbjct: 303 LRDAGRPCLKEASMAKLFASEMAEKVCSDAIQIHGGYGYVSDFPVERIYRDVRVCQIYEG 362 Query: 374 THDVHALILGRAQTG 388 D+ L++GR+ G Sbjct: 363 ASDIQRLVIGRSLDG 377 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: 337 Number of extensions: 11 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: 379 Length adjustment: 30 Effective length of query: 363 Effective length of database: 349 Effective search space: 126687 Effective search space used: 126687 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