Align 3-oxoadipate CoA-transferase (EC 2.8.3.6) (characterized)
to candidate WP_007507152.1 R2APBS1_RS03875 3-oxoadipate--succinyl-CoA transferase subunit B
Query= reanno::WCS417:GFF1319 (259 letters) >NCBI__GCF_000230695.2:WP_007507152.1 Length = 264 Score = 281 bits (720), Expect = 7e-81 Identities = 142/253 (56%), Positives = 179/253 (70%) Query: 2 AYSTNEMMTVAAARRLKNGSVCFVGIGLPSKAANLARLTSSPDVVLIYESGPIGAKPSVL 61 A + +E MTVAAAR LKN +CFVGIGLPS A NLARLT +P +VLIYESG IG +P V+ Sbjct: 3 ACTRDEWMTVAAARLLKNRDICFVGIGLPSAACNLARLTHAPQIVLIYESGTIGTRPDVM 62 Query: 62 PLSIGDGELAETADTVVPTGEIFRYWLQGGRIDVGFLGAAQVDRFGNINTTVVGDYHQPK 121 PLSIGDGELA+TA VVP EIF Y+LQ GR+D+GFLGAAQ+DR GN+N+TV+G Y P Sbjct: 63 PLSIGDGELAQTAACVVPLPEIFSYYLQAGRVDIGFLGAAQIDRHGNLNSTVIGPYETPS 122 Query: 122 VRLPGAGGAPEIAGSAKSVLIILKQSARSFVDKLDFITSVGHGEGGDSRKRLGLPGAGPV 181 RLPGAGGAPEIA A+ V ++L+ S RSFV++L F +S G+ +G +R R G G GP Sbjct: 123 TRLPGAGGAPEIAQHARQVFVMLRASKRSFVERLAFRSSAGYLDGHGARARSGAAGGGPR 182 Query: 182 GIITDLCIMEPEAGTHEFVVTALHPGVTREQVVAATGWAIRFADQVDTTAEPTDVELTAL 241 +ITD ++ P + E + AL G T E+ AA GW ++ AD++DT A P+ EL L Sbjct: 183 AVITDFGMLAPHPESEELQLVALFEGATVEEARAAIGWPLQLADRIDTIAPPSAHELDTL 242 Query: 242 RDLEARTAAAHGQ 254 R L ART AH + Sbjct: 243 RALHARTREAHAR 255 Lambda K H 0.317 0.135 0.394 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: 274 Number of extensions: 16 Number of successful extensions: 1 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: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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