Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_043528348.1 JH15_RS07090 3-oxoadipyl-CoA thiolase
Query= SwissProt::P45363 (394 letters) >NCBI__GCF_000759345.1:WP_043528348.1 Length = 405 Score = 317 bits (812), Expect = 4e-91 Identities = 180/396 (45%), Positives = 255/396 (64%), Gaps = 14/396 (3%) Query: 12 RTAIGTFGGALSALQATDIGTTVLKALIERT-GIAPEQVSEVILGQVLTAG-CGQNPARQ 69 R+A+G FGGALS+L+ D+ + +AL+ R + P + +VI+G AG +N AR Sbjct: 11 RSAVGKFGGALSSLRPDDLAARIFEALLARAPDLDPAAIEDVIMGCANQAGEDNRNVARM 70 Query: 70 TTLMAGLPHTVPAMTINKVCGSGLKAVHLAMQAVACGDAEIVIAGGQESMSQSSHVLPRS 129 + L+AGLP +VP T+N++CGS + A+ A +AV G+AE++IAGG ESMS++ +VL ++ Sbjct: 71 SLLLAGLPTSVPGTTLNRLCGSSMDAIGTAARAVRAGEAELMIAGGVESMSRAPYVLGKA 130 Query: 130 REG----QRMGDWPMKDTMIVDGLWDAFNQCHMGVTAENIAKKYAFTREAQDAFAAASQQ 185 Q M D + I L + M TAEN+A+++ +RE QD FA SQ Sbjct: 131 DTAFSRTQTMEDTTIGWRFINPLLRKQYGVDSMPETAENVAEQFKISREDQDRFAYDSQL 190 Query: 186 KAEAAIQSGRFADEIIPVSIPQRKGDPLVFDTDEFPRPGTTAETLGRLRPAF-----DKQ 240 K + A +GR A EI+PV IP+RK DPLVFDTDE PR TT E L L F Sbjct: 191 KTKRAQDNGRLAREIVPVEIPRRKQDPLVFDTDEHPRE-TTLEKLASLPTPFRAAGSSVM 249 Query: 241 GTVTAGNASGINDGAAMVVVMKESKAKELGLTPMARLVAFSSAGVDPAIMGTGPIPASTD 300 G+VTAGNASG+NDGAA ++V E+ K LTPMAR+ ++AGV+P IMG GP+PA+ + Sbjct: 250 GSVTAGNASGVNDGAAAMIVASEAAVKRYNLTPMARIHGMATAGVEPRIMGIGPVPATQN 309 Query: 301 CLKKAGWAPADLDLVEANEAFAAQAMSVNQEMGWDLS--KVNVNGGAIAIGHPIGASGAR 358 LK+ G + LD +E NEAFAAQA++ +E+G D + +VN NGGAIA+GHP+G SGAR Sbjct: 310 LLKRLGMSLDQLDHIELNEAFAAQALACLRELGIDDNDPRVNPNGGAIALGHPLGMSGAR 369 Query: 359 VLVTLLYEMQKRDAKKGLATLCIGGGQGVALAVERL 394 ++ + ++E+ + L T+CIG GQG+A +ER+ Sbjct: 370 IVTSAMHELHLTGGRFALCTMCIGVGQGIATLIERV 405 Lambda K H 0.317 0.131 0.380 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: 367 Number of extensions: 13 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: 394 Length of database: 405 Length adjustment: 31 Effective length of query: 363 Effective length of database: 374 Effective search space: 135762 Effective search space used: 135762 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 (21.7 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