Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_012536805.1 AFE_RS08595 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-11802 (255 letters) >NCBI__GCF_000021485.1:WP_012536805.1 Length = 261 Score = 102 bits (255), Expect = 6e-27 Identities = 84/257 (32%), Positives = 127/257 (49%), Gaps = 20/257 (7%) Query: 3 IANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQA----VEAKARELGDNARFAVA 58 + + +V+GA+ GLG A A++L AGA+V + QA V A + G A+ A Sbjct: 6 LTGRRALVTGASGGLGQAIAEILAAAGAQVAVHYRKGQAEAEQVVAAIQGKGGKAQAFQA 65 Query: 59 DISDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGLASFAKVINVNLIGS 118 DISD A + + AFG L LVN AG+ G V+G P + KV+ V+L+G Sbjct: 66 DISDPAAVERLLREIDGAFGGLDILVNNAGMDGPRAVVGDDDPQ---LWEKVLAVDLVGP 122 Query: 119 FNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARE 178 + R A M + GVIIN S+ + G +AY ++K ++ T A+E Sbjct: 123 YYCARAAIPRMEKCGC------GVIINITSVHEFIPWEGYSAYTSAKAGLSMFTKTLAQE 176 Query: 179 LARFGIRVMTIAPGIFETPM---MAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIE 235 A GIRV+ IAPG +TP+ + G D ++ L + RLG P+E +A + Sbjct: 177 TADKGIRVVAIAPGAIKTPINKAVWGNPDSLK-DLDDKIAM-ERLGTPEEIGHVAAFLAS 234 Query: 236 N--SMLNGEVIRLDGAL 250 + S + G I +DG + Sbjct: 235 DLASYVTGTTIAVDGGM 251 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: 125 Number of extensions: 9 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: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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