Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate HSERO_RS04630 HSERO_RS04630 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__HerbieS:HSERO_RS04630 Length = 254 Score = 303 bits (776), Expect = 2e-87 Identities = 155/248 (62%), Positives = 191/248 (77%), Gaps = 1/248 (0%) Query: 8 FIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQ 67 ++V+GAASGLGAATA+ L+ AGAKV+L D+N A E LG NARF + D++ E +AQ Sbjct: 8 YVVTGAASGLGAATAEQLIRAGAKVVLADVNPVAGEKMQATLGANARFVLTDVTSETSAQ 67 Query: 68 SAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFNLLRLAAA 127 A S+ G++ GLVNCAGI EK+LGK G H L SF + +N+NL+GSFN+ RLAA Sbjct: 68 EVFGVA-SSMGAVVGLVNCAGIAPGEKLLGKGGVHRLDSFMRALNINLVGSFNMARLAAQ 126 Query: 128 AMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRVM 187 ++ G AD +GERGVII+TASIAA+DGQ+GQ AYAASKG + S+TLP ARELAR GIRV+ Sbjct: 127 HISAGPADATGERGVIIHTASIAAFDGQMGQVAYAASKGGVVSMTLPMARELARHGIRVV 186 Query: 188 TIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLNGEVIRLD 247 TIAPGI ETPMM GM +EV SL+ VPFPPRLG+P E+A L HI+EN LNGEVIR+D Sbjct: 187 TIAPGIIETPMMLGMPEEVLESLSRNVPFPPRLGKPSEFAGLVMHILENRYLNGEVIRMD 246 Query: 248 GALRMAAK 255 GALRM+AK Sbjct: 247 GALRMSAK 254 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: 196 Number of extensions: 7 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