Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012278034.1 SHAL_RS15295 3-oxoadipyl-CoA thiolase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_000019185.1:WP_012278034.1 Length = 423 Score = 319 bits (818), Expect = 8e-92 Identities = 178/400 (44%), Positives = 258/400 (64%), Gaps = 10/400 (2%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALER-AGVKPEQVSEVIMGQVLTA 59 + DV I A RT +G++G L+ + A +L A+ IKA +ER V +Q ++++G + Sbjct: 24 LKDVYICDAIRTPIGRYGSGLSSVRADDLAALPIKALIERNPDVDWQQCDDLLLGCANQS 83 Query: 60 GS-GQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENM 118 G +N AR A + AGLP VP T+N++CGSGL A+ AA AI G+A++++AGG E+M Sbjct: 84 GEDNRNIARMAGLLAGLPVEVPGCTVNRLCGSGLNALGDAARAIRTGEADLMIAGGVESM 143 Query: 119 SAAPHVLPGSRDGFRMGDAKLVDTM---IVDGLWDV-YNQYHMGITAENVAKEYGITREA 174 S AP V+P + F TM ++ +D Y M TAEN+A+++ I+REA Sbjct: 144 SRAPFVMPKATSPFARSTEFYDTTMGWRFINPEFDKHYGTEAMPQTAENLAQDFAISREA 203 Query: 175 QDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKP 234 QD FA+ SQ KA +AQ+AG FD EIVPV IP R+G+P F DE +R ++L+ +S LKP Sbjct: 204 QDRFALWSQQKAASAQEAGLFDNEIVPVTIPVRRGEPTVFSKDEHLRL-SSLEKLSSLKP 262 Query: 235 AFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPV 294 FDK G +TA NASG+NDGAAA+++ SA + L P A I A AGV P+VMG+GPV Sbjct: 263 LFDK-GAITAGNASGINDGAAALLLASAEGVVQHKLKPRAKILGMAVAGVPPRVMGLGPV 321 Query: 295 PASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGW--DTSKVNVNGGAIAIGHPIG 352 PA+ + L R + D+DL+E NEAFAAQAL +++G D ++N GGAIA+GHP+G Sbjct: 322 PATNKLLKRLNLSLDDMDLLEFNEAFAAQALTCIRELGLKDDDPRINPQGGAIALGHPLG 381 Query: 353 ASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 SG R+ T +++++R + L ++C+G G G+A+ +ER Sbjct: 382 MSGARLATTAVNQLERTQGRYALCTMCVGVGQGIAMIIER 421 Lambda K H 0.315 0.131 0.369 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: 382 Number of extensions: 17 Number of successful extensions: 6 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: 393 Length of database: 423 Length adjustment: 31 Effective length of query: 362 Effective length of database: 392 Effective search space: 141904 Effective search space used: 141904 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: 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