Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate RR42_RS03440 RR42_RS03440 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11802 (255 letters) >FitnessBrowser__Cup4G11:RR42_RS03440 Length = 252 Score = 289 bits (740), Expect = 3e-83 Identities = 154/255 (60%), Positives = 184/255 (72%), Gaps = 3/255 (1%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADI 60 M I + FIV+G ASGLG +A+ML AG KV++ DLN A A A ELG +F D+ Sbjct: 1 MEIRDNVFIVTGGASGLGEGSARMLAAAGGKVVIADLNEAAGTALAAELG--GKFVRCDV 58 Query: 61 SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFN 120 S E Q+ V AA + G L GLVNCAGI A K +GK GPH L +F K I VNLIG+FN Sbjct: 59 SSEADGQATV-AAATTLGRLAGLVNCAGIATANKTVGKNGPHPLDAFDKTIRVNLIGTFN 117 Query: 121 LLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELA 180 ++RLAAAAM + D GERGVIINTAS+AA+DGQIGQAAYAASKG + ++TL AR+L+ Sbjct: 118 MIRLAAAAMVQNTPDAQGERGVIINTASVAAFDGQIGQAAYAASKGGVVAMTLAIARDLS 177 Query: 181 RFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLN 240 R G+R MTIAPG+FETPM+ GM EV+ +L VPFPPRLGRP EYA L II N+MLN Sbjct: 178 RDGVRCMTIAPGLFETPMLLGMPQEVQDALGKMVPFPPRLGRPAEYAKLVESIIANTMLN 237 Query: 241 GEVIRLDGALRMAAK 255 GEVIRLDGA+RM K Sbjct: 238 GEVIRLDGAIRMQPK 252 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: 185 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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