Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate 203460 SO4382 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__MR1:203460 Length = 241 Score = 98.2 bits (243), Expect = 1e-25 Identities = 78/252 (30%), Positives = 125/252 (49%), Gaps = 19/252 (7%) Query: 5 NKHFIVSGAASGLGAATAQMLVEAGAKVMLV----DLNAQAVEAKARELGDNARFAVADI 60 N +V+G++ G+G A A L AG + L A A A+ R LG N D+ Sbjct: 2 NNRVLVTGSSRGIGKAIALKLAAAGHDIALHYHSNQAAADASAAELRALGVNVSLLKFDV 61 Query: 61 SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFN 120 +D A ++A++A + A G+ +G+V AGI + A + VI+ NL G +N Sbjct: 62 ADRVAVRAALEADIEANGAYYGVVLNAGI-NRDNAFPAMSE---AEWDSVIHTNLDGFYN 117 Query: 121 LLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELA 180 ++ M + + G II AS++ G GQ Y+ASK + T + ELA Sbjct: 118 VIHPCVMPMVQAR-----KGGRIITLASVSGIAGNRGQVNYSASKAGLIGATKALSLELA 172 Query: 181 RFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIEN--SM 238 + I V IAPG+ ET M+A + ++ L VP R+G+P E AALA ++ + + Sbjct: 173 KRKITVNCIAPGLIETDMVADIPKDMVEQL---VPM-RRMGKPNEIAALAAFLMSDDAAY 228 Query: 239 LNGEVIRLDGAL 250 + +VI ++G + Sbjct: 229 ITRQVISVNGGM 240 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: 110 Number of extensions: 8 Number of successful extensions: 3 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: 241 Length adjustment: 24 Effective length of query: 231 Effective length of database: 217 Effective search space: 50127 Effective search space used: 50127 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