Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate 5210126 Shew_2570 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= reanno::ANA3:7024494 (389 letters) >FitnessBrowser__PV4:5210126 Length = 389 Score = 731 bits (1886), Expect = 0.0 Identities = 365/389 (93%), Positives = 378/389 (97%) Query: 1 MNSLYTSLNFGLGEEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGV 60 M LY+SLNFGLGE++DMLRDAV+ FA +EIAPIAAKVD +NAFPNE+WPVLG MGLLGV Sbjct: 1 MTQLYSSLNFGLGEDIDMLRDAVRSFAANEIAPIAAKVDQENAFPNELWPVLGEMGLLGV 60 Query: 61 TVPEEYGGANMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPK 120 TVPEEYGGA+MGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPK Sbjct: 61 TVPEEYGGADMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPK 120 Query: 121 LVSGEHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTD 180 LVSGEHIGALAMSEPNAGSDVVSMKL ARKEGDRYILNGNKMWITNGPDA+TYVIYAKTD Sbjct: 121 LVSGEHIGALAMSEPNAGSDVVSMKLSARKEGDRYILNGNKMWITNGPDADTYVIYAKTD 180 Query: 181 LTKGAHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVK 240 + KG HGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFED EVPEENILGGLNNGVK Sbjct: 181 MDKGPHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVK 240 Query: 241 VLMSGLDYERVVLSGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMN 300 VLMSGLDYERVVLSGGPLGIM ACMDIVVPYIHEREQFGKSIG+FQLVQGKLADMYTGMN Sbjct: 241 VLMSGLDYERVVLSGGPLGIMTACMDIVVPYIHEREQFGKSIGQFQLVQGKLADMYTGMN 300 Query: 301 AAKAYVYSVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLL 360 AAK+YVY+VAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLL Sbjct: 301 AAKSYVYNVAKSCDRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLL 360 Query: 361 RDAKLYEIGAGTSEIRRMLIGRELFNESK 389 RDAKLYEIGAGTSEIRRMLIGRELFNESK Sbjct: 361 RDAKLYEIGAGTSEIRRMLIGRELFNESK 389 Lambda K H 0.316 0.135 0.388 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: 617 Number of extensions: 9 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: 389 Length of database: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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 (21.6 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