Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_055437597.1 ASC41_RS15620 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >NCBI__GCF_001418085.1:WP_055437597.1 Length = 600 Score = 228 bits (581), Expect = 3e-64 Identities = 145/392 (36%), Positives = 210/392 (53%), Gaps = 26/392 (6%) Query: 5 ELTEEQVMIRDMARDFARGEIAPHAQAWEKAGW-IDDALVAKMGELGLLGMVVPEEWGGT 63 + +EEQ M+++ +F EI PH +E + + + ++ K GELG LG+ VPE +GG Sbjct: 29 DFSEEQNMMKEAVTEFNDREIIPHKPRFEAKDYALTEEVMRKAGELGFLGVAVPEAYGGL 88 Query: 64 YVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGC 123 + +V+ L + IS+G G+ H +G P+ YGTE QKQ ++ LASG+ G Sbjct: 89 GMGFVSTVLTCDYISSGTGSFSTAFGAHTGIGTMPITLYGTEAQKQKYVPKLASGEWFGS 148 Query: 124 FCLTEPQAGSEAHNLRTRAEL-RDGQ-WVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKG 181 +CLTEP AGS+A++ +T A L DG+ + ING K ++SN + IVFA + D K Sbjct: 149 YCLTEPGAGSDANSGKTTAVLSEDGKSYKINGQKMWISNAGFCTVMIVFARLEDD---KN 205 Query: 182 LSAFLVPTDTP-GFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNL 240 ++ F+V D G + EHK+GIRAS T V N+ +P N+L RG+G IA++ L Sbjct: 206 ITGFIVENDAANGITMGEEEHKLGIRASSTRQVFFNDTVVPIENMLAGRGEGFKIAMNAL 265 Query: 241 EGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLI 300 GRI +AA L R + YA +R QF PI + ++ LA+M T A Sbjct: 266 NVGRIKLAAACLDSQRRIVTHGVKYAMERKQFKTPIADFGAIKMKLAEMATNAYAGESAT 325 Query: 301 LHAAR-------LRSAGKPCLSEA------------SQAKLFASEMAEKVCSSAIQIHGG 341 AA+ LR A EA S K+ SE + IQI GG Sbjct: 326 YRAAKNIEDRIALREAAGNTHQEAELKGVEEYAIECSILKVAVSEDVQNCADEGIQIFGG 385 Query: 342 YGYLEDYPVERYYRDARITQIYEGSSEIQRMV 373 G+ E+ P+E +RDARI +IYEG++EI RM+ Sbjct: 386 MGFSEETPMESAWRDARIARIYEGTNEINRML 417 Lambda K H 0.319 0.134 0.394 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: 480 Number of extensions: 26 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: 383 Length of database: 600 Length adjustment: 34 Effective length of query: 349 Effective length of database: 566 Effective search space: 197534 Effective search space used: 197534 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: 51 (24.3 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