Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_001592305.1:WP_068170917.1 Length = 393 Score = 751 bits (1938), Expect = 0.0 Identities = 372/391 (95%), Positives = 384/391 (98%) Query: 6 NLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVP 65 NLPGLNFQLGEDIDALRDAVR+FAQAEIAPRAA+IDKSDQFPMD WRKMG+LGVLGITVP Sbjct: 3 NLPGLNFQLGEDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVP 62 Query: 66 EQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLIS 125 EQYGGA MGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGN+AQKAKYL KLIS Sbjct: 63 EQYGGANMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLIS 122 Query: 126 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPEL 185 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNG+KMWITNGPDADTLVVYAK+EPE+ Sbjct: 123 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEM 182 Query: 186 GARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLM 245 GARGVTAFLIEKGM GFSIAQKLDKLGMRGSHTGELVFQ+VEVPA+N+LGGLN GAKVLM Sbjct: 183 GARGVTAFLIEKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLM 242 Query: 246 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGR 305 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQA R Sbjct: 243 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAAR 302 Query: 306 SFAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGR 365 SFAYTVAKNLD+LGT+HVRQVRKDCASVILW AEKATWMAGEGVQIYGGNGYINEYPLGR Sbjct: 303 SFAYTVAKNLDLLGTEHVRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGR 362 Query: 366 LWRDAKLYEIGAGTSEIRRMLIGRELFAETC 396 LWRDAKLYEIGAGTSEIRRMLIGRELFAETC Sbjct: 363 LWRDAKLYEIGAGTSEIRRMLIGRELFAETC 393 Lambda K H 0.318 0.136 0.400 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: 689 Number of extensions: 17 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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