Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 6938693 Sama_2796 acyl-CoA dehydrogenase-like protein (RefSeq)
Query= reanno::SB2B:6937192 (389 letters) >FitnessBrowser__SB2B:6938693 Length = 391 Score = 198 bits (503), Expect = 2e-55 Identities = 124/377 (32%), Positives = 191/377 (50%), Gaps = 8/377 (2%) Query: 8 LNFG--LGEDVDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEE 65 LNF L E+ M+RD V+E+A+ ++ +RD F E+ + G++GLLG T+ EE Sbjct: 12 LNFNSLLTEEERMIRDMVHEYAQDKLMARVLMANRDEHFDREIMNELGELGLLGATLPEE 71 Query: 66 YGGVNMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGE 125 YG N Y+++ + EI R + + S+L ++ IY G EAQR KYLPKL +GE Sbjct: 72 YGCANANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYTYGTEAQRRKYLPKLATGE 131 Query: 126 HIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTDLDKGP 185 +G ++EP+ GSD MK A + Y + G KMWITN P A +V++AK D Sbjct: 132 WVGCFGLTEPDVGSDPAGMKTRAERIDGGYRITGAKMWITNSPIADVFVVWAKLD----- 186 Query: 186 HGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVKVLMSG 245 I F++E+G KG S + K +R S T E+V ++ EV E+ +L + G+K Sbjct: 187 GAIRGFVLEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEVGEDALLPNV-EGLKGPFGC 245 Query: 246 LDYERVVLSGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSY 305 L+ R ++ G LG C Y +R+QF + + QL Q KLADM T + Sbjct: 246 LNKARYGIAWGALGAAEFCWHAARQYGLDRIQFNRPLAANQLYQKKLADMQTEITTGLFA 305 Query: 306 VYNVARACDRGETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKL 365 R D + + + + A +A A + GGNG +E+ R + + + Sbjct: 306 CLQAGRLMDVDALPVEAISLIKRNSCGKALDIARIARDMHGGNGISDEFHVIRHVMNLEA 365 Query: 366 YEIGAGTSEIRRMLIGR 382 GT +I +++GR Sbjct: 366 VNTYEGTHDIHALILGR 382 Lambda K H 0.318 0.137 0.396 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: 389 Number of extensions: 17 Number of successful extensions: 4 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: 389 Length of database: 391 Length adjustment: 31 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 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