Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_093396488.1 BM091_RS13350 acetyl-CoA C-acyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_900114975.1:WP_093396488.1 Length = 414 Score = 294 bits (752), Expect = 4e-84 Identities = 180/413 (43%), Positives = 239/413 (57%), Gaps = 24/413 (5%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M VIVSA RT VG++ GSL + A +L A+V+K A+ RAG+ P+QV EV+MGQ G Sbjct: 1 MEKAVIVSAVRTPVGRYLGSLRSVEAYDLAALVLKEAVARAGLSPDQVDEVVMGQSYQNG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 N AR A +KAG P +P +T+++ C SGL+ V AA+ I G AE+VVAGG E+MS Sbjct: 61 EYVNIARMALLKAGWPDSIPGITLDRRCCSGLEVVRYAASLIATGQAEVVVAGGVESMSN 120 Query: 121 APHVLP-------GSRDGFRM--GDAKLVDTMIVDGLWDVYNQYH----------MGITA 161 A LP G R+G GD K+ + D + + M A Sbjct: 121 AEFYLPGHIKWGIGGREGMPRGHGDLKIWGIPLYDRIQRARVMHQPIERYGVLQSMMTWA 180 Query: 162 ENVAKEYGITREAQDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVR 221 E A+E GI+RE D +A+ S A A + GKF EE+VPV + G F+ DE R Sbjct: 181 ETAAREEGISREECDAWALRSHQNACRAWREGKFQEEVVPVPVRGSDGSDTLFERDETPR 240 Query: 222 QGATLDSMSGLKPAFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYAN 281 + +L+ +S LKP G TA N+S NDGAAAV+VMS KA+E GL P+A + Sbjct: 241 EDTSLEKLSRLKPVL--GGVCTAGNSSSENDGAAAVLVMSERKAREFGLRPMARFLACDV 298 Query: 282 AGVDPKVMGMGPVPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDT---SKV 338 A DP+ + A K+ LSR +D+ L+EI EAFAAQ LA +QMG D ++ Sbjct: 299 AACDPRKTYLSVPIAVKKVLSRTGLKLEDMGLIEIQEAFAAQVLADMKQMGLDEKDYDRI 358 Query: 339 NVNGGAIAIGHPIGASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVE 391 NVNG I++GHPI +G R+LVTLLHEMKRR K GL +C GGG+G+A +E Sbjct: 359 NVNGSGISLGHPIACTGTRVLVTLLHEMKRRGVKYGLECICGGGGLGIAAVME 411 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: 379 Number of extensions: 15 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: 393 Length of database: 414 Length adjustment: 31 Effective length of query: 362 Effective length of database: 383 Effective search space: 138646 Effective search space used: 138646 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