Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_039790199.1 CEJ45_RS12595 isovaleryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_002213425.1:WP_039790199.1 Length = 394 Score = 608 bits (1569), Expect = e-179 Identities = 298/391 (76%), Positives = 341/391 (87%), Gaps = 1/391 (0%) Query: 6 NLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVP 65 +LPGLNF GEDI ALR+AV FAQ EIAPRAA+ID+SDQFPMDLW+K+GDLGVLGITV Sbjct: 3 HLPGLNFDHGEDIAALREAVAAFAQTEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVG 62 Query: 66 EQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLIS 125 E+YGGA +GYLAH++AMEEISRASASVGLSYGAHSNLCVNQI RNGNE QK KYL KLIS Sbjct: 63 EEYGGAGLGYLAHIIAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPKLIS 122 Query: 126 GEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPEL 185 G+ +GALAMSEP AGSDV+SMKL+A+ KG Y+LNGSKMWITNGPDAD LVVYAKT+ + Sbjct: 123 GDFIGALAMSEPNAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLDA 182 Query: 186 GARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLM 245 GARG+TAFL+EKG KGFS+AQKLDKLGMRGSHTGELVFQD EVP ENVLGG+ +G VLM Sbjct: 183 GARGMTAFLVEKGYKGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLM 242 Query: 246 SGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGR 305 SGLD+ER+VL+GGPLGIMQ+ MD V+PY+HDRKQFGQ+IGEFQL+QGK+ADMY+ + A + Sbjct: 243 SGLDFERSVLSGGPLGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACK 302 Query: 306 SFAYTVAKNLDML-GTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLG 364 ++ Y V + D D VR +RKD A IL+ AEKATWMAGE +Q GGNGYINEYP+G Sbjct: 303 AYVYAVGQACDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVG 362 Query: 365 RLWRDAKLYEIGAGTSEIRRMLIGRELFAET 395 RLWRDAKLYEIGAGTSEIRRMLIGRELFA+T Sbjct: 363 RLWRDAKLYEIGAGTSEIRRMLIGRELFADT 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: 598 Number of extensions: 16 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: 396 Length of database: 394 Length adjustment: 31 Effective length of query: 365 Effective length of database: 363 Effective search space: 132495 Effective search space used: 132495 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 Sep 24 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