Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate RR42_RS26910 RR42_RS26910 isovaleryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS26910 Length = 393 Score = 665 bits (1716), Expect = 0.0 Identities = 323/389 (83%), Positives = 359/389 (92%) Query: 7 LPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPE 66 LPGLNF LGEDID LR+ VR++AQAE+APRAA+ID++DQFPMD W+KMGDLGVLGITV E Sbjct: 4 LPGLNFHLGEDIDMLRETVRNWAQAELAPRAAEIDRTDQFPMDAWKKMGDLGVLGITVAE 63 Query: 67 QYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISG 126 +YGGA MGYLAHM+AMEEISRASASVGLSYGAHSNLCVNQI+RNG AQKA+YL KL+SG Sbjct: 64 EYGGANMGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTAAQKARYLPKLVSG 123 Query: 127 EHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELG 186 + +GALAMSEP AGSDV+SMKL+A+ KG +Y+LNG+KMWITNGPD D LVVYAKTEP+LG Sbjct: 124 DWIGALAMSEPNAGSDVVSMKLRADFKGDHYVLNGTKMWITNGPDCDVLVVYAKTEPDLG 183 Query: 187 ARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMS 246 ARG+TAF++EKGMKGFS+AQKLDKLGMRGSHTGELVFQDVEVP EN+LGG N GAKVLMS Sbjct: 184 ARGMTAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPVENILGGENLGAKVLMS 243 Query: 247 GLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRS 306 GLDYERAVL+GGP+GIMQ+ MD + PYIHDRKQFGQSIGEFQLIQGKVADMYT LQA RS Sbjct: 244 GLDYERAVLSGGPVGIMQACMDVITPYIHDRKQFGQSIGEFQLIQGKVADMYTTLQAARS 303 Query: 307 FAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRL 366 + YTV KNLD LG DHVRQVRKDCA+VIL+ AEKATWMAGE VQI GGNGYINEYP+GRL Sbjct: 304 YLYTVGKNLDSLGKDHVRQVRKDCAAVILYTAEKATWMAGESVQILGGNGYINEYPVGRL 363 Query: 367 WRDAKLYEIGAGTSEIRRMLIGRELFAET 395 WRDAKLYEIGAGTSEIRRMLIGREL+AET Sbjct: 364 WRDAKLYEIGAGTSEIRRMLIGRELYAET 392 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: 637 Number of extensions: 12 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 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