Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_013450480.1 CALNI_RS01735 acetyl-CoA C-acyltransferase
Query= uniprot:A0A2Z5MFE9 (400 letters) >NCBI__GCF_000183405.1:WP_013450480.1 Length = 392 Score = 290 bits (742), Expect = 5e-83 Identities = 171/393 (43%), Positives = 240/393 (61%), Gaps = 32/393 (8%) Query: 19 GALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQAGEDNRNVARMSALLAGLP 78 G KD+R DDL + ++R+ VD + ++DVI GCA GE NV+R+++ +AGLP Sbjct: 20 GKFKDLRPDDLLGKVLAETVKRSQ-VDPQLIEDVIIGCAFPEGEQGMNVSRVASFIAGLP 78 Query: 79 ADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKAASAFTRQA 138 D P TINR C SG+ ++ AA + AG A ++AGGVESMT P K ++ Sbjct: 79 IDVPAMTINRFCSSGLQSIAIAAERVMAGFADCIVAGGVESMTMIPMGGVKYSA------ 132 Query: 139 EIHDTTIGWRFVNP--LMKRQYGVDSMPETAENVAEQFGISRADQDAFALASQQKAARAQ 196 NP + K SM TAE VAE++GISR DQD FAL S KA +A Sbjct: 133 ------------NPGLISKWPETYASMGITAELVAEKYGISREDQDQFALNSHMKAVKAI 180 Query: 197 RDGTLAQEIVGVEI----AQKKGDAIR----VTLDEHPRE-TSLESLARLKGVVRPDGTV 247 ++G A EIV VE+ KG+ ++ VT+D+ RE T+ E LA+LK V + +G+V Sbjct: 181 KEGKFADEIVPVEVEYTAVDPKGNIVKTKEVVTIDDGAREDTTYEGLAKLKPVFKLNGSV 240 Query: 248 TAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLR 307 TAGN+S + DGA A L+ S+ ++Y L+ AR VG + GVEP IMGIGP + +L+ Sbjct: 241 TAGNSSQMTDGAAACLVVSEDFLKRYNLKPMARFVGFSARGVEPEIMGIGPVKSIPVVLQ 300 Query: 308 QLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVT 367 + G+T + + +IELNEAFA+Q LAV+R LGL + +N NGGAIALGHPLG +G +L Sbjct: 301 KAGLTFNDIGLIELNEAFAAQSLAVIRNLGLNPE--IINVNGGAIALGHPLGCTGTKLTA 358 Query: 368 TALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 T L++++R N ++ + +MCIG G G A + E L Sbjct: 359 TLLNEMKRRNVKYGMVSMCIGGGMGAAGIFENL 391 Lambda K H 0.319 0.134 0.386 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: 381 Number of extensions: 12 Number of successful extensions: 4 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: 400 Length of database: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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 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