Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_086509636.1 BZY95_RS09155 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_002151265.1:WP_086509636.1 Length = 393 Score = 558 bits (1439), Expect = e-164 Identities = 274/384 (71%), Positives = 317/384 (82%), Gaps = 1/384 (0%) Query: 9 WIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGAT 68 W DP L QL E+ERMV +A+ + QDKL PRVLEA RHE+ D I EMGE+GLLGAT Sbjct: 9 WEDPFRLIDQLDEDERMVHQTAHDYCQDKLMPRVLEANRHERFDREIMNEMGELGLLGAT 68 Query: 69 IPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKL 128 I + YG +G+NYV YGLIAREVER+DSGYRS MSVQSSLVM PI+ FG+EAQ++KYLPKL Sbjct: 69 I-DGYGCAGMNYVSYGLIAREVERVDSGYRSAMSVQSSLVMYPIHAFGSEAQREKYLPKL 127 Query: 129 ASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA 188 A+GEW+GCFGLTEP+HGSDPG M TRA + + G+RL G+K WITNSPIADVFVVWA+D+ Sbjct: 128 ATGEWVGCFGLTEPDHGSDPGGMSTRATRTENGWRLNGTKTWITNSPIADVFVVWARDEE 187 Query: 189 GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGPFTCL 248 G I GF+LEK +GLSAP I GK LRASITG+I M +V V +E P V GLKGPF+CL Sbjct: 188 GVINGFILEKDMKGLSAPKIEGKFSLRASITGQIAMQDVEVSDEQRLPGVTGLKGPFSCL 247 Query: 249 NSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGC 308 N AR+GI+WG++GAAEACWH ARQYTLDR+QFGRPLAANQLIQKKLADMQTEI L LQ Sbjct: 248 NRARFGIAWGSMGAAEACWHAARQYTLDRKQFGRPLAANQLIQKKLADMQTEIALGLQAA 307 Query: 309 LRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVV 368 LR+GRM D G E S++KRN+CGKALDIAR+ARDM GGNGI+DE+ V RH++NLE V Sbjct: 308 LRVGRMIDAGQLVPEAISLIKRNNCGKALDIARVARDMHGGNGIADEYHVIRHMMNLEAV 367 Query: 369 NTYEGTHDVHALILGRAQTGIQAF 392 NTYEGTHDVHALILGRAQTGIQAF Sbjct: 368 NTYEGTHDVHALILGRAQTGIQAF 391 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: 543 Number of extensions: 10 Number of successful extensions: 2 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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