Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate RR42_RS00870 RR42_RS00870 isovaleryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__Cup4G11:RR42_RS00870 Length = 396 Score = 657 bits (1696), Expect = 0.0 Identities = 320/395 (81%), Positives = 358/395 (90%) Query: 1 MSIPANLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVL 60 M LPGL F LGEDI+ LR+ V ++AQAE+APRAA+ID++DQFPMD W+KMGDLGVL Sbjct: 1 MIATTELPGLKFDLGEDIEMLRETVCNWAQAELAPRAAEIDRTDQFPMDAWKKMGDLGVL 60 Query: 61 GITVPEQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYL 120 GITV E+YGGA MGYLAHM+AMEEISRASASVGLSYGAHSNLCVNQI+RNG AQKA+YL Sbjct: 61 GITVAEEYGGANMGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTAAQKARYL 120 Query: 121 SKLISGEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAK 180 KL+SG+ +GALAMSEP AGSDV+SMKL+A+ KG +Y+LNG+KMWITNGPD D LVVYAK Sbjct: 121 PKLVSGDWIGALAMSEPNAGSDVVSMKLRADFKGDHYVLNGTKMWITNGPDCDVLVVYAK 180 Query: 181 TEPELGARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQG 240 TEP+LGARG+TAF++EKGMKGFS+AQKLDKLGMRGSHTGELVFQDVEVP EN+LGG N G Sbjct: 181 TEPDLGARGMTAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPVENILGGENLG 240 Query: 241 AKVLMSGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTV 300 AKVLMSGLDYERAVL+GGP+GIMQ+ MD + PYIHDRKQFGQSIGEFQLIQGKVADMYT Sbjct: 241 AKVLMSGLDYERAVLSGGPVGIMQACMDVITPYIHDRKQFGQSIGEFQLIQGKVADMYTT 300 Query: 301 LQAGRSFAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINE 360 LQA RS+ YTV KNLD LG DHVRQVRKDCA+VIL+ AEKATWMAGE VQI GGNGYINE Sbjct: 301 LQAARSYLYTVGKNLDSLGKDHVRQVRKDCAAVILYTAEKATWMAGESVQILGGNGYINE 360 Query: 361 YPLGRLWRDAKLYEIGAGTSEIRRMLIGRELFAET 395 YP+GRLWRDAKLYEIGAGTSEIRRMLIGRELF++T Sbjct: 361 YPVGRLWRDAKLYEIGAGTSEIRRMLIGRELFSQT 395 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: 624 Number of extensions: 13 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: 396 Length adjustment: 31 Effective length of query: 365 Effective length of database: 365 Effective search space: 133225 Effective search space used: 133225 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