Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate WP_057507563.1 ABB28_RS04915 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-11693 (386 letters) >NCBI__GCF_001431535.1:WP_057507563.1 Length = 388 Score = 249 bits (636), Expect = 9e-71 Identities = 149/387 (38%), Positives = 222/387 (57%), Gaps = 12/387 (3%) Query: 1 MDHRLTPELEELRRTVEEFAHDVVAPKIGDFYERHE----FPYEIVREMGRMGLFGLPFP 56 M + +T ELEE ++ E A D ++ R + FP E + + G +G GL Sbjct: 1 MSNSMTTELEEAQQAYREAARDFAQAELAPHAARWDAEGIFPREAIAKAGELGFCGLYMD 60 Query: 57 EEYGGMGGDYLALGIALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCS 116 E GG G L + +EELA VD S A + ++ + + +G A +A W L + Sbjct: 61 PEVGGSGLSRLDAAVVIEELANVDPSTAAYVSIH-NMASWMVSTWGQQALRAAWGADLAA 119 Query: 117 GEILGAFGLTEPDGGSDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVT 176 G L ++ LTEP GSDA + +TTA D +++V+NG+K FI+ +G T L+ V A T Sbjct: 120 GIRLASYCLTEPGAGSDAASLKTTAVRDG--DDYVLNGSKAFISGAGA--TELLVVMART 175 Query: 177 GRKPDGKPLISSIIVPSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRG 236 G G IS+I VP+ PG + K+GWN+ TR ++F +VRVP NLLGE+G G Sbjct: 176 GGAGAGG--ISAIAVPADLPGISYGRKEEKMGWNSQPTRGITFENVRVPVGNLLGEEGGG 233 Query: 237 YAQFLRILDEGRIAISALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMK 296 + ++ LD GRI I+A + G AQG +D + +Y GER FG+ + +QA+QFK+ADM ++ Sbjct: 234 FKLAMKGLDGGRINIAACSLGAAQGALDAARRYMGERRQFGKALAEFQALQFKLADMAIE 293 Query: 297 AHMARVGWRDAASRLVAG-EPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVA 355 AR AA +L AG A+AK +++ EA QIHGGYG++ EYP+ Sbjct: 294 LVAARQMVHTAARKLDAGASDANVWCAMAKRFATDAGFTICNEALQIHGGYGYIREYPIE 353 Query: 356 RMWRDSKILEIGEGTSEVQRMLIAREL 382 R+ RDS++ +I EGT+E+ R+++AR L Sbjct: 354 RLLRDSRVHQILEGTNEIMRVIVARHL 380 Lambda K H 0.318 0.136 0.402 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: 401 Number of extensions: 17 Number of successful extensions: 5 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: 386 Length of database: 388 Length adjustment: 30 Effective length of query: 356 Effective length of database: 358 Effective search space: 127448 Effective search space used: 127448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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