Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate N515DRAFT_1006 N515DRAFT_1006 3-oxoacyl-[acyl-carrier protein] reductase
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_1006 Length = 248 Score = 87.8 bits (216), Expect = 2e-22 Identities = 80/258 (31%), Positives = 118/258 (45%), Gaps = 22/258 (8%) Query: 3 IANKHFIVSGAASGLGAATAQMLVEAGAKVML----VDLNAQAVEAKARELGDNARFAVA 58 + K +V+GA+ G+GA A+ L GA V++ A AV + G A Sbjct: 4 LKGKVALVTGASKGIGAGIAKALAAEGAAVVVNYASSKAGADAVVDAITKAGGKAVAVKG 63 Query: 59 DISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGS 118 D++ AQ+ DAAV FG L LVN +G+ + H F K NVN++G Sbjct: 64 DVAQAADAQAIADAAVKEFGRLDILVNNSGVYEFAPLEQITEDH----FHKQFNVNVLGL 119 Query: 119 FNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARE 178 + AA M EG G IIN S+ G + Y A+KGA+ ++T +RE Sbjct: 120 LLTTQAAAKHMGEG--------GSIINIGSLVTRIVPPGGSVYTATKGAVDAITGVLSRE 171 Query: 179 LARFGIRVMTIAPGIFET--PMMAG-MSDEVRASLAAGVPFPPRLGRPQEYAALARHII- 234 L IRV + PG+ ET + AG + + A P R+G+PQ+ A +A + Sbjct: 172 LGPRKIRVNALNPGMVETEGTVTAGFIGSDFHQEAIAHTPL-GRIGQPQDIATIAVFLAS 230 Query: 235 -ENSMLNGEVIRLDGALR 251 ++ L GE + G R Sbjct: 231 DDSYWLTGEKLYAAGGAR 248 Lambda K H 0.318 0.131 0.358 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: 123 Number of extensions: 5 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: 255 Length of database: 248 Length adjustment: 24 Effective length of query: 231 Effective length of database: 224 Effective search space: 51744 Effective search space used: 51744 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: 46 (22.3 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