Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_086511720.1 BZY95_RS20380 KR domain-containing protein
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_002151265.1:WP_086511720.1 Length = 255 Score = 96.3 bits (238), Expect = 6e-25 Identities = 79/262 (30%), Positives = 119/262 (45%), Gaps = 22/262 (8%) Query: 3 IANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKAR---ELGDNARFAVAD 59 + +K IV+G G+G A + G+KV ++D + A E G AR AD Sbjct: 4 LEDKTVIVTGGGGGIGRAVCRRFAAEGSKVAVLDRDLDAARRTVEVIAEAGGQARAYGAD 63 Query: 60 ISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSF 119 I+D A V+ + G LVN AG L K P A + +I VNL G+ Sbjct: 64 ITDYAAIVDTVERIEAELGVPRVLVNNAGFDRFMPFL-KTEP---ALWESLIAVNLTGAL 119 Query: 120 NLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179 N+ + M E G +IN AS AA G G+A YAA K + L+ AREL Sbjct: 120 NMHHVVLPRMIEAGG------GKVINVASDAARVGSSGEAVYAACKAGLLGLSKTLAREL 173 Query: 180 ARFGIRVMTIAPGIFETPMMAGMSDEVR------ASLAAGVPFPPRLGRPQEYAALARHI 233 A G+ + + PG +T ++ G ++ R + VP R+G+P++Y + + Sbjct: 174 ATKGVTLNVVCPGPTDTALLQGFAETSRDPEKLLEAFRNAVPM-RRIGQPEDYPGIIALL 232 Query: 234 IEN--SMLNGEVIRLDGALRMA 253 + + G+VI + G L MA Sbjct: 233 ASDDADFITGQVISVSGGLTMA 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: 115 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 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