Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_101588592.1 BJEO58_RS06050 SDR family NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_900169175.1:WP_101588592.1 Length = 250 Score = 240 bits (612), Expect = 2e-68 Identities = 136/256 (53%), Positives = 170/256 (66%), Gaps = 7/256 (2%) Query: 1 MHIANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADI 60 M I ++ V+G ASGLG AT Q +VE G K + DL A LGD+ F D+ Sbjct: 1 MQIKDQVAFVTGGASGLGLATVQAIVERGGKAVAFDLKGSDEIAA---LGDDVIFVEGDV 57 Query: 61 SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGSFN 120 ++E Q+A++ S G L +VNCAGI G+ +V G+ G L F KV+ VNLIG+FN Sbjct: 58 TNEAQVQAAIERT-SELGDLRIVVNCAGIGGSHRVSGRNGVFPLDHFTKVVTVNLIGTFN 116 Query: 121 LLRLAAAAMAEGAADESGE-RGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179 + RLAAA M A D GE RGV+INTAS AA+DGQ+GQAAY+ASKG I +TLP AR+L Sbjct: 117 VTRLAAAHMQ--AIDPVGEERGVVINTASAAAFDGQVGQAAYSASKGGIVGMTLPIARDL 174 Query: 180 ARFGIRVMTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSML 239 A IRVMT+APGIF TP+M G S+E SL VP P RLG P+E+ +A I+ENSML Sbjct: 175 ASSQIRVMTVAPGIFHTPLMLGASEETLKSLGDQVPHPSRLGVPEEFGLMAAQIVENSML 234 Query: 240 NGEVIRLDGALRMAAK 255 NGE IRLDGA+RMA + Sbjct: 235 NGETIRLDGAIRMAPR 250 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: 160 Number of extensions: 5 Number of successful extensions: 3 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: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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