Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate RR42_RS28565 RR42_RS28565 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25670 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS28565 Length = 377 Score = 538 bits (1386), Expect = e-157 Identities = 264/374 (70%), Positives = 313/374 (83%) Query: 5 ELTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTY 64 E +E+Q MIRD AR FA +AP A W++AG + +VA+MG LGLLGM+VPEEWGGTY Sbjct: 4 EFSEQQTMIRDTARTFASERLAPCAAEWDRAGQLPAEVVAEMGALGLLGMIVPEEWGGTY 63 Query: 65 VDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCF 124 DY+AYALA+EEI+AG A LMS+HNSVGCGP+L+YGT+ QK+ +L LASG+ IG F Sbjct: 64 TDYIAYALAIEEIAAGCAACATLMSVHNSVGCGPILHYGTQAQKERYLPRLASGEIIGAF 123 Query: 125 CLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSA 184 CLTEPQAGSEAHNLRTRA D WV++G+KQFV+NG+RA +AIVFA T+P GK+GLSA Sbjct: 124 CLTEPQAGSEAHNLRTRARATDNGWVLSGSKQFVTNGQRAGVAIVFAATEPAQGKRGLSA 183 Query: 185 FLVPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGR 244 F+VPTDTPGF V E KMGIRASDTCA+TL++C +P LLGE G+GL IALSNLEGGR Sbjct: 184 FVVPTDTPGFSVHTPERKMGIRASDTCAITLDDCQVPHDALLGEPGEGLRIALSNLEGGR 243 Query: 245 IGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILHAA 304 IGIAAQALGIAR+AFEAA YA +RVQF +P+ EH +ANMLADM T LNAARLL+ AA Sbjct: 244 IGIAAQALGIARSAFEAACRYAAERVQFGRPLREHAPIANMLADMATELNAARLLVHRAA 303 Query: 305 RLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIYE 364 +R+AG+PCLSEASQAKL+ASE+AE+VCS A+QIHGGYGYLEDYPVER+YRDARITQIYE Sbjct: 304 HMRTAGQPCLSEASQAKLYASELAERVCSKALQIHGGYGYLEDYPVERHYRDARITQIYE 363 Query: 365 GSSEIQRMVIAREL 378 G+SEIQRM+IAR L Sbjct: 364 GTSEIQRMLIARTL 377 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: 433 Number of extensions: 13 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 353 Effective length of database: 347 Effective search space: 122491 Effective search space used: 122491 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 17 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