Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_050654880.1 C1M55_RS10590 3-oxoadipate--succinyl-CoA transferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4591 (259 letters) >NCBI__GCF_002893965.1:WP_050654880.1 Length = 261 Score = 186 bits (473), Expect = 3e-52 Identities = 101/241 (41%), Positives = 143/241 (59%), Gaps = 1/241 (0%) Query: 4 TTNEMMTVAAARRLKNGSVCFVGIGLPSKAANLARLTSSPDVVLIYESGPIGAKPSVLPL 63 T+ E + AAR L F G+GLP+ A +LAR TS+PDV LIYESG GA PS + Sbjct: 11 TSTETIVAVAARELAGKRRVFAGVGLPTLAVDLARHTSNPDVELIYESGVCGAHPSAMAE 70 Query: 64 SIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVVGDYHAPKVR 123 I D + A++V+ +F Y LQGG +DVGFLGAAQ+DR G++NT+ +GD+ P VR Sbjct: 71 GIADSVVVSGAESVLSMAALFGYVLQGGNVDVGFLGAAQIDRTGSLNTSFIGDWKNPTVR 130 Query: 124 LPGAGGAPEIAGSAKSVLIILKQSS-RSFVDKLDFITSVGHGEGGDSRKRLGLPGAGPVG 182 LPGAGGA EI +A + +++++ SF LDF TS S K + GAG Sbjct: 131 LPGAGGAVEIIANAAEIFVVMRRHDLSSFPAALDFCTSPSPARAHASGKGIMPAGAGVTK 190 Query: 183 IITDLCIMEPEAGTHEFVVTALHPGVTREQVVDATGWAIRFADQVEQTAEPTEVELTALR 242 + T+L ++ + E +T++H G++ QV +ATGW + AD V T P+ E+ LR Sbjct: 191 VFTNLGVLTHQGPGGELELTSVHEGISVHQVREATGWDLAVADHVTVTTPPSGTEIDLLR 250 Query: 243 D 243 + Sbjct: 251 N 251 Lambda K H 0.316 0.135 0.393 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: 207 Number of extensions: 7 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: 259 Length of database: 261 Length adjustment: 24 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 (21.6 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