Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_089215596.1 CHB69_RS08555 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_900188185.1:WP_089215596.1 Length = 404 Score = 317 bits (812), Expect = 4e-91 Identities = 187/400 (46%), Positives = 252/400 (63%), Gaps = 18/400 (4%) Query: 6 IVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAGSGQNP 65 IV+ RTAVGKFGG+L+ + A ELGAV++KA +ER + P +V +V+ Q G+G+ P Sbjct: 8 IVAPIRTAVGKFGGTLSPLTAGELGAVILKALVERTKIDPARVDDVVFSQ--GYGNGEAP 65 Query: 66 A--RQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSAAPH 123 A + + AGLP VP +++ CGSGL+AV+ AA + G +++VVAGG E+MS H Sbjct: 66 AIGHWSWLAAGLPLEVPGYQLDRRCGSGLQAVVNAAMMVQTGMSDVVVAGGVESMSNVEH 125 Query: 124 VLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGI------TAENVAKEYGITREAQDE 177 R G R G+ L D + L + G+ TAEN+AK+YGITREA D Sbjct: 126 YSTDIRKGVRAGNLTLHDRLTRGRLMSQPIE-RFGVISGMIETAENLAKDYGITREAADA 184 Query: 178 FAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFD 237 +AV S +A AA G F++E+VPV +PQRKGDP+ F DE R AT++S+ L+ Sbjct: 185 YAVRSHQRAAAAWDKGLFNDELVPVSVPQRKGDPIVFDHDEGYRADATMESLGKLRAL-- 242 Query: 238 KAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPAS 297 + G VTA NAS ND AAA +V++ K +ELGL P+A S A AG DP MG+GPVPA Sbjct: 243 EGGVVTAGNASQQNDAAAACLVVAEDKLEELGLEPIAWYHSSAAAGCDPSRMGIGPVPAV 302 Query: 298 KRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGW--DTSK---VNVNGGAIAIGHPIG 352 +R +R D+DL+E+NEAFA Q LAV + GW D S+ +NVNG I++GHPIG Sbjct: 303 ERLFARNGLGWGDIDLVELNEAFAPQVLAVLKGWGWSDDDSRGDILNVNGSGISLGHPIG 362 Query: 353 ASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 A+G RIL L E+ RRD + GL ++CIGGG G+A ER Sbjct: 363 ATGGRILANLTRELVRRDGRYGLETMCIGGGQGIAAIFER 402 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: 415 Number of extensions: 17 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: 404 Length adjustment: 31 Effective length of query: 362 Effective length of database: 373 Effective search space: 135026 Effective search space used: 135026 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