Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_012170588.1 AZC_RS10675 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000010525.1:WP_012170588.1 Length = 246 Score = 113 bits (283), Expect = 3e-30 Identities = 80/246 (32%), Positives = 125/246 (50%), Gaps = 16/246 (6%) Query: 9 IVSGAASGLGAATAQMLVEAGAKVMLV--DLNAQAVEAKARELGDNARFAVADISDEQAA 66 +V+GA+ G+G A A+ L +AGA V++ L+ +E +++ + D+SD + A Sbjct: 11 LVTGASRGIGLAVARRLADAGATVVINARQLDEGLLEGWPQDVRERIVLEAGDVSDPEVA 70 Query: 67 QSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLAA 126 + V S F L LVN AGI+ A + G A ++VN+ + ++ + AA Sbjct: 71 RRIVRGLFSRFKRLDILVNNAGIMRAAMI----GMIPDADVRATLDVNVGSAIHMTQAAA 126 Query: 127 AAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRV 186 MA G I+N ASI +G GQ AYAASK + T AA+ELA G+RV Sbjct: 127 RLMARSG-------GAIVNVASIVGLEGASGQLAYAASKAGVVGATRAAAKELAPKGVRV 179 Query: 187 MTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIE--NSMLNGEVI 244 +APG ET M A + EV+A + R G P++ A + + + + G+V+ Sbjct: 180 NAVAPGYIETDMTANLGAEVKAQTLKTIGL-GRTGTPEDVADVVLFLCSDLSRYVTGQVL 238 Query: 245 RLDGAL 250 R+DG + Sbjct: 239 RVDGGM 244 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: 128 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: 246 Length adjustment: 24 Effective length of query: 231 Effective length of database: 222 Effective search space: 51282 Effective search space used: 51282 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 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