Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_036834462.1 N784_RS09610 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000775615.1:WP_036834462.1 Length = 379 Score = 235 bits (599), Expect = 2e-66 Identities = 132/375 (35%), Positives = 212/375 (56%), Gaps = 5/375 (1%) Query: 15 LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74 ++ Q TEE+ M+R FA ++AP V + + + + ++MG++GL+G IPEQYG Sbjct: 1 MNLQFTEEQHMMRKMVRDFANKEVAPIVQQMDQEDYFPIELIKQMGDIGLMGIPIPEQYG 60 Query: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134 GSG+++ Y + E+ ++ + ++SV +S+ PI FGTE QKQKY+PKLASGE++ Sbjct: 61 GSGMDFPSYIIAIHELSKVSASVGVILSVHTSVGTNPILYFGTEEQKQKYIPKLASGEFL 120 Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----D 190 G F LTEP GSD GS+ +A + Y L GSK++ITN AD F+V+A+ D+ Sbjct: 121 GAFALTEPGAGSDAGSLKMKAVREGEEYILNGSKVFITNGEKADTFIVFARTDSNAGNKG 180 Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVP-EENIFPDVRGLKGPFTCLN 249 + F++E+ G K+G+ S T + DN +P E+ + + G K LN Sbjct: 181 VTAFIVERNTSGFEIGKKEHKMGMNGSGTVTLNFDNCRIPAEQRLGEEGEGFKIAMANLN 240 Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309 R GI+ +LG AEA A Y +R+QFG+P+A NQ I KLADM T + A Sbjct: 241 VGRIGIAAQSLGIAEAALEHAVGYAKEREQFGKPIARNQGISFKLADMATSVEAAKLLTY 300 Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369 ++ +G + S+ K + A+++A A + GG G ++++ V R + +V Sbjct: 301 HAANLRHQGIDCGKEASMAKMTASQAAMNVATEAIQVYGGYGYTEDYPVERFFRDAKVCE 360 Query: 370 TYEGTHDVHALILGR 384 YEGT+++ +++G+ Sbjct: 361 IYEGTNEIQRVVIGK 375 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: 14 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 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