Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__Pedo557:CA265_RS08355 Length = 254 Score = 99.8 bits (247), Expect = 5e-26 Identities = 80/259 (30%), Positives = 127/259 (49%), Gaps = 28/259 (10%) Query: 3 IANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVA---D 59 + NK +V+G SG+G A A +L + GA+V +++L + + E+ N A + D Sbjct: 4 LKNKKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSYGCD 63 Query: 60 ISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSF 119 +SD QA V A + G+++ L+N AGI +GK A F +V+ VN+ G + Sbjct: 64 VSDHQA----VAAVFNEIGNINILINNAGIAH----IGKADTTDEADFDRVMRVNVKGVY 115 Query: 120 NLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179 N L A + GVIIN ASIAA G + Y+A+KGA+ ++T+ A++ Sbjct: 116 NCLHAAIPQIRLSGG------GVIINMASIAALIGLPDRFVYSAAKGAVKAITMSVAKDY 169 Query: 180 ARFGIRVMTIAPGIFETPMMAGMSD--------EVRASLAAGVPFPPRLGRPQEYAALAR 231 IR +I+P TP + G E+ L+ P R+ +P+E ALA Sbjct: 170 IGENIRCNSISPARVHTPFVDGFLQKNYPDNIPEMFEKLSKTQPI-GRMAKPEEVGALAL 228 Query: 232 HII--ENSMLNGEVIRLDG 248 ++ E S + G +DG Sbjct: 229 YLCSDEASFITGCDYPIDG 247 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: 121 Number of extensions: 8 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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: 47 (22.7 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