Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 201 bits (511), Expect = 3e-56 Identities = 122/371 (32%), Positives = 189/371 (50%), Gaps = 6/371 (1%) Query: 6 LTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYV 65 LTEE+ MIRDM ++A+ ++ + D ++ ++GELGLLG +PEE+G Sbjct: 18 LTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLPEEYGCANA 77 Query: 66 DYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCFC 125 +YV+Y L EI D + MS+ +S+ P+ YGTE Q++ +L LA+G+ +GCF Sbjct: 78 NYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLATGEWVGCFG 137 Query: 126 LTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSAF 185 LTEP GS+ ++TRAE DG + I GAK +++N A + +V+A D + F Sbjct: 138 LTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAKLD-----GAIRGF 192 Query: 186 LVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGRI 245 ++ G + E K +RAS T + ++N + E LL +GL L R Sbjct: 193 VLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALL-PNVEGLKGPFGCLNKARY 251 Query: 246 GIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILHAAR 305 GIA ALG A + AA Y DR+QF++P+ +Q LADM T + L A R Sbjct: 252 GIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFACLQAGR 311 Query: 306 LRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIYEG 365 L + S K + A + A +HGG G +++ V R+ + YEG Sbjct: 312 LMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEAVNTYEG 371 Query: 366 SSEIQRMVIAR 376 + +I +++ R Sbjct: 372 THDIHALILGR 382 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: 338 Number of extensions: 20 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: 383 Length of database: 391 Length adjustment: 30 Effective length of query: 353 Effective length of database: 361 Effective search space: 127433 Effective search space used: 127433 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