Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_068168283.1 HTA01S_RS06660 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_001592305.1:WP_068168283.1 Length = 392 Score = 557 bits (1435), Expect = e-163 Identities = 283/392 (72%), Positives = 325/392 (82%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M D+VIVSAARTAVGKFGGSLAK PA ELG++VIK L R G+ + V EVIMGQVL AG Sbjct: 1 MEDIVIVSAARTAVGKFGGSLAKTPATELGSIVIKELLARTGLPVDAVGEVIMGQVLAAG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 GQNPARQA +KAG+ PA+TIN VCGSGLKAVMLAA A+ GD+EIV+AGGQENMSA Sbjct: 61 CGQNPARQAMMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSA 120 Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180 +PHVL GSRDG RMGD K+ DTMIVDGLWDVYNQYHMGITAENVAK GITRE QD A Sbjct: 121 SPHVLNGSRDGQRMGDWKMTDTMIVDGLWDVYNQYHMGITAENVAKAQGITREMQDALAA 180 Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240 GSQ KA AAQ AGKF +EIV V IPQRKGDPV F +DEF+ T + ++GL+PAFDK+G Sbjct: 181 GSQQKAAAAQAAGKFKDEIVGVSIPQRKGDPVLFNSDEFINAKTTAEVLAGLRPAFDKSG 240 Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300 +VTA NASG+NDGAAAV+VM+A KA LGLTPLA I ++ +G+DP +MGMGPVPAS++A Sbjct: 241 SVTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGPVPASQKA 300 Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360 L+RA W D+D+ E+NEAFAAQA AV+ + D +KVNVNGGAIAIGHPIGASGCRILV Sbjct: 301 LARAGWKASDVDVFELNEAFAAQACAVNMALDIDPAKVNVNGGAIAIGHPIGASGCRILV 360 Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 TLLHEM+RR AKKGLA+LCIGGGMGV+LAVER Sbjct: 361 TLLHEMQRRGAKKGLAALCIGGGMGVSLAVER 392 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: 528 Number of extensions: 16 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: 393 Length of database: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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 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