Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_004315427.1 C665_RS13930 isovaleryl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000310185.1:WP_004315427.1 Length = 393 Score = 189 bits (480), Expect = 1e-52 Identities = 124/385 (32%), Positives = 196/385 (50%), Gaps = 19/385 (4%) Query: 15 LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74 L+ L E +RD+ F ++APR E R + +++++G++G+ G T+ E+YG Sbjct: 6 LNFNLGETIDALRDTLQAFCAAEIAPRAAEIDRVNEFPADLWKKLGDLGVHGMTVSEEYG 65 Query: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134 G+ + Y+ + + E+ R + S+L + I GTEAQKQKYLPKL SGE + Sbjct: 66 GTDMGYLAHIVAMEEISRASASVGLSYGAHSNLCINQIRRNGTEAQKQKYLPKLISGEHV 125 Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----D 190 G ++EPN GSD SM RA + + L GSKMWITN AD VV+AK D Sbjct: 126 GALAMSEPNAGSDVVSMKLRADRKGDRFILNGSKMWITNGGDADTLVVYAKTDIAAGPKG 185 Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV----RGLKGPFT 246 I F++EKG +G S K+G+R S T + D+V VP EN+ RG++ + Sbjct: 186 ITAFIIEKGMKGFSHGTHLDKLGMRGSNTFPLFFDDVEVPAENVLGGEANIGRGVQVLMS 245 Query: 247 CLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQ 306 L+ R +S G LG AC Y +R+QF P+ QL+Q K+AD+ + + Sbjct: 246 GLDYERAVLSGGPLGIMAACMDVVVPYLHERKQFDTPIGEFQLMQGKVADLYSTWSACRA 305 Query: 307 GCLRLGRMKDEGTAAVEITSIMKRNSCG-------KALDIARMARDMLGGNGISDEFGVA 359 +G+ D + +++++ G KA +A A LGG G ++E+ Sbjct: 306 YAYAVGQACDR----TDHARTLRKDAAGVILYTAEKATWMAGEAIQTLGGVGYTNEYATG 361 Query: 360 RHLVNLEVVNTYEGTHDVHALILGR 384 R + ++ GT ++ +++GR Sbjct: 362 RLWRDAKLYEIGAGTSEIRRMLIGR 386 Lambda K H 0.320 0.137 0.413 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: 347 Number of extensions: 16 Number of successful extensions: 4 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: 393 Length of database: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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