Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_011842744.1 RSPH17029_RS19805 acetyl-CoA C-acyltransferase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000015985.1:WP_011842744.1 Length = 386 Score = 235 bits (600), Expect = 1e-66 Identities = 153/398 (38%), Positives = 221/398 (55%), Gaps = 23/398 (5%) Query: 4 LICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGEDN 63 +I A RTP G + GAL +L +A I + + R G+ VE+++ GC AG Sbjct: 7 VIAGAARTPMGAFQGALKGRTGVELGSAAISAALAR-AGLAPEAVEEVVMGCVLPAGL-G 64 Query: 64 RNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAP 123 + AR A L AGLP++VP +T+N++CGS + A A I++G +++AGG+ESM+ AP Sbjct: 65 QAPARQAALGAGLPLSVPCATLNKVCGSGMKAAMAAHDMIRAGSAGIVVAGGMESMSNAP 124 Query: 124 FVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDAF 183 +++ KA + + F++ L A +M AE+ A +Q R QDA+ Sbjct: 125 YLLDKARGGYRIGHG---RVLDHMFLDGLEDAYDRGRAMGTFAEDCAEAYQFTRDAQDAY 181 Query: 184 ALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHP---RPDTTLATLAKLKGV 240 AL S R AA A G FA E+ + V DE P RP+ + +L+ Sbjct: 182 ALASLARAQAAIAEGRFAAEVVAVD---------GVAVDEAPGRARPEK----IPQLRPA 228 Query: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 R GTVTA N+S ++DGA AL++AS AA+ L P A + G A+ AP + P Sbjct: 229 FREGGTVTAANSSSISDGAAALVIASAGAAEAQGLTPLATIRGHASHAQAPNLFTTAPIF 288 Query: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 A+ K+L +VG + A++D+ E+NEAFA +A MRDL LP D VN NGGA A+GHP+G Sbjct: 289 AIGKLLERVGWSAAEVDLFEINEAFAVVAMAAMRDLDLPHD--KVNVNGGACALGHPIGC 346 Query: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIE 398 SGAR+V T I L G R + ++CIG G+ AL +E Sbjct: 347 SGARIVVTLIEALRARGLRRGVASLCIGGGEATALAVE 384 Lambda K H 0.320 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: 398 Number of extensions: 24 Number of successful extensions: 5 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: 401 Length of database: 386 Length adjustment: 31 Effective length of query: 370 Effective length of database: 355 Effective search space: 131350 Effective search space used: 131350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. 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