Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate 16329 b2221 acetyl-CoA:acetoacetyl-CoA transferase, alpha subunit (NCBI)
Query= CharProtDB::CH_021928 (231 letters) >FitnessBrowser__Keio:16329 Length = 220 Score = 186 bits (472), Expect = 3e-52 Identities = 90/204 (44%), Positives = 136/204 (66%), Gaps = 10/204 (4%) Query: 18 DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGLAALLMAGSVRKVVCS 77 DG TIMVGGF G PS L++ L+ +G RDLT+I+N+ + G+ L++ G VRKV+ S Sbjct: 17 DGMTIMVGGFMGIGTPSRLVEALLESGVRDLTLIANDTAFVDTGIGPLIVNGRVRKVIAS 76 Query: 78 F----PRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFFSPTGYGTLLAEG 133 P + +G++++ +VPQG L E+I G+G+G F +PTG GT++ EG Sbjct: 77 HIGTNPETGRRMI------SGEMDVVLVPQGTLIEQIRCGGAGLGGFLTPTGVGTVVEEG 130 Query: 134 KETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMAMAAKTAIAQVD 193 K+T +DG+ ++LE PL AD ALI+AH+ D GNLTY+ +ARNF P++A+AA + + D Sbjct: 131 KQTLTLDGKTWLLERPLRADLALIRAHRCDTLGNLTYQLSARNFNPLIALAADITLVEPD 190 Query: 194 QVVELGELDPEHIITPGIFVQRVV 217 ++VE GEL P+HI+TPG + ++ Sbjct: 191 ELVETGELQPDHIVTPGAVIDHII 214 Lambda K H 0.318 0.135 0.381 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: 133 Number of extensions: 5 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: 231 Length of database: 220 Length adjustment: 22 Effective length of query: 209 Effective length of database: 198 Effective search space: 41382 Effective search space used: 41382 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 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