Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000009985.1:WP_011383120.1 Length = 389 Score = 223 bits (568), Expect = 7e-63 Identities = 139/375 (37%), Positives = 201/375 (53%), Gaps = 5/375 (1%) Query: 15 LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74 L+ L E M+RDS FA ++APR E R + ++ +G +GLLG T+ E+YG Sbjct: 8 LNFDLGETADMMRDSVAAFAATEIAPRAAEIDRSNEFPNELWPRLGAMGLLGITVDEKYG 67 Query: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134 G+G+ Y+ + + E+ R + S+L + I GTEAQK KYLPKL SGE+I Sbjct: 68 GAGMGYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLISGEYI 127 Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AG--D 190 G ++EPN GSD SM +A K Y L G+KMWITN P ADV VV+AK D AG Sbjct: 128 GALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVTAGPRG 187 Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLN 249 I F++EK ++G S K+G+R S TGE+V + VPEEN+ V +G+ + L+ Sbjct: 188 ITAFLVEKTFKGFSVAQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGVNVLMSGLD 247 Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309 R ++ G LG AC Y +R QFG+P+ QL+Q KLADM T Sbjct: 248 YERVVLTGGPLGIMAACMDVVVPYVHERTQFGQPIGTFQLMQGKLADMYTTFNACRAYTY 307 Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369 + + D G + + + + KA +A A LGGNG +E+ R L + ++ Sbjct: 308 AVAKACDRGETSRKDAAGVILYGAEKATWMALEAIQTLGGNGYINEYATGRLLRDAKLYE 367 Query: 370 TYEGTHDVHALILGR 384 GT ++ +++GR Sbjct: 368 IGAGTSEIRRMLIGR 382 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: 356 Number of extensions: 14 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: 389 Length adjustment: 31 Effective length of query: 362 Effective length of database: 358 Effective search space: 129596 Effective search space used: 129596 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 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