Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_010960235.1 MCA_RS04555 3-oxoacyl-ACP reductase FabG
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000008325.1:WP_010960235.1 Length = 239 Score = 91.7 bits (226), Expect = 1e-23 Identities = 84/249 (33%), Positives = 122/249 (48%), Gaps = 22/249 (8%) Query: 9 IVSGAASGLGAATAQMLVEAGAKVMLV----DLNAQAVEAKARELGDNARFAVADISDEQ 64 +VSG + G+GAA + L G V + +A+ V R G +A D+ D Sbjct: 5 LVSGGSGGIGAAICRRLALDGLHVWVHYHGHRQSAEQVVDAIRVGGGSAEAIGFDVCDAA 64 Query: 65 AAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRL 124 AA +A+ A + A + LVN AGI + + +VI+V+L G FNL + Sbjct: 65 AAAAAI-ATMCAERPIQVLVNNAGIHDDAVFPAMRSDQ----WHRVIDVSLNGFFNLTQP 119 Query: 125 AAAAMAEGAADESGER-GVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFG 183 M ER G I+N +S+AA G GQ Y+A+KGA+ S T A ELA G Sbjct: 120 LVMPMIR-------ERWGRIVNISSVAALTGNRGQVNYSAAKGALHSATRSLALELASRG 172 Query: 184 IRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIEN--SMLNG 241 + V +APGI ET M D RA++ VP R GRP+E A L + + + + G Sbjct: 173 VTVNAVAPGIIETGMAESAFD--RAAIERLVPM-KRAGRPEEVADLVAFLASDRAAYITG 229 Query: 242 EVIRLDGAL 250 +VI ++G + Sbjct: 230 QVISINGGI 238 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: 105 Number of extensions: 5 Number of successful extensions: 1 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: 239 Length adjustment: 24 Effective length of query: 231 Effective length of database: 215 Effective search space: 49665 Effective search space used: 49665 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