Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_057508928.1 ABB28_RS12395 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_001431535.1:WP_057508928.1 Length = 256 Score = 266 bits (680), Expect = 3e-76 Identities = 139/256 (54%), Positives = 179/256 (69%), Gaps = 1/256 (0%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGD-NARFAVAD 59 M ++N +++G SGLG A A+ LV G KV L DLN + A LG NA + + Sbjct: 1 MQLSNVRAVITGGVSGLGLAVAEHLVAQGGKVALFDLNDEKGAAAVAALGQANASYQQVN 60 Query: 60 ISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSF 119 +SDE A A++ A + G L+ VNCAGI+GA +VLGK+GP L+ F + VNL+GSF Sbjct: 61 VSDEAAVAEAIEQAHAFLGGLNVAVNCAGILGAGRVLGKEGPMPLSGFQSTVMVNLVGSF 120 Query: 120 NLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179 N+ + AA + A GERGVIINTASIAAY+GQIGQAAYAASKG + S+TLP AREL Sbjct: 121 NVAKAAANRIQHNDAGTDGERGVIINTASIAAYEGQIGQAAYAASKGGVVSMTLPMAREL 180 Query: 180 ARFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSML 239 +RFGIRV TIAPG+F TPM+ GM V+ SLAA +PFP RLG+P+++A+L +I+ N+ L Sbjct: 181 SRFGIRVNTIAPGVFWTPMVDGMPPAVQQSLAASIPFPSRLGKPEDFASLVAYILGNTYL 240 Query: 240 NGEVIRLDGALRMAAK 255 NGE IRLDGA R+A K Sbjct: 241 NGETIRLDGATRLAPK 256 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: 178 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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