Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_028311754.1 H566_RS0112785 3-oxoadipyl-CoA thiolase
Query= uniprot:D8ITH5 (401 letters) >NCBI__GCF_000482785.1:WP_028311754.1 Length = 401 Score = 603 bits (1554), Expect = e-177 Identities = 306/398 (76%), Positives = 340/398 (85%) Query: 3 ALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGED 62 A +CDAIRTPFGRYGG+L VRADDL A PIR+LM RNP VDW+ ++D++YGCANQAGED Sbjct: 4 AYLCDAIRTPFGRYGGSLSGVRADDLGAVPIRALMARNPSVDWAALDDVIYGCANQAGED 63 Query: 63 NRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRA 122 NRNV RM+ LLAGLP VPG+TVNRLCGSSLDA AARAI++GEVQL+IAGGVESM+RA Sbjct: 64 NRNVGRMSALLAGLPPEVPGTTVNRLCGSSLDATASAARAIRAGEVQLVIAGGVESMSRA 123 Query: 123 PFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQDA 182 PFVMGKA AF+RSA + DTTIGWRFVNPLMKA +G+DSMPETAENVATDF + RADQDA Sbjct: 124 PFVMGKATEAFSRSAKVEDTTIGWRFVNPLMKAMHGVDSMPETAENVATDFDVARADQDA 183 Query: 183 FALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVVR 242 FALRSQQR AAAQAAG + EI P+TI QK+GD LVV+ DEH RP+TTLA LAKLKGVVR Sbjct: 184 FALRSQQRAAAAQAAGRLSQEITPVTIAQKRGDALVVSADEHLRPETTLAALAKLKGVVR 243 Query: 243 PDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPAV 302 PDGTVTAGNASGVNDGA ALLLAS A + LKPRAR++ A AGVAPRIMGFGPAPA+ Sbjct: 244 PDGTVTAGNASGVNDGAAALLLASEAGAARHGLKPRARIVASAVAGVAPRIMGFGPAPAI 303 Query: 303 RKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGASG 362 KVLA L L Q+DVIELNEAFAAQ LAV R GL DD A VNPNGGAIA+GHPLGASG Sbjct: 304 TKVLALAKLRLDQIDVIELNEAFAAQALAVTRAHGLADDDARVNPNGGAIALGHPLGASG 363 Query: 363 ARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400 ARLV A+++LER+GGRY LCTMCIGVGQGIALVIERV Sbjct: 364 ARLVIAALHELERTGGRYGLCTMCIGVGQGIALVIERV 401 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: 562 Number of extensions: 13 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: 401 Length of database: 401 Length adjustment: 31 Effective length of query: 370 Effective length of database: 370 Effective search space: 136900 Effective search space used: 136900 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 09 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