Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_090445655.1 BLS63_RS14265 acetyl-CoA C-acetyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_900100495.1:WP_090445655.1 Length = 393 Score = 576 bits (1484), Expect = e-169 Identities = 284/392 (72%), Positives = 336/392 (85%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60 M +VVIV ATRTAIG FQG+LA + A +LGA VIRRLL+ TGL+G +V+EVI+GQVL AG Sbjct: 1 MNDVVIVCATRTAIGRFQGALAGVSAVDLGAVVIRRLLDSTGLAGHEVNEVIMGQVLAAG 60 Query: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQA+I AGLP+ VPALT+NKVCGSGL+A+HL AQAIRCGDAEV+IAGG E+MS Sbjct: 61 AGQNPARQAAIKAGLPYTVPALTINKVCGSGLEAIHLAAQAIRCGDAEVMIAGGQESMSQ 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180 APYVL AR GLRMGH +++DSMI DGLWDAFNDYHMGITAENL ++YG++RE+QD++A Sbjct: 121 APYVLAQARQGLRMGHKELLDSMIHDGLWDAFNDYHMGITAENLAEQYGVTREQQDSYAL 180 Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240 SQQ+A A GRF EI P+ +PQR G+ + DEQP +G +AE L +LKPAFKKDG Sbjct: 181 RSQQRASTARAAGRFVAEIAPVQVPQRGGETLRVDCDEQPASGASAEGLARLKPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300 SVTAGNAS+LNDGAAAV+LMSA KA+ALGLPV+A+I AYA+AGVDP++MGIGPV A+ C Sbjct: 241 SVTAGNASTLNDGAAAVLLMSASKAEALGLPVMARIKAYASAGVDPSVMGIGPVFASDLC 300 Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360 L KAGW+LEQLDLIEANEAFA Q+L V REL WD D+VNVNGGAIALGHP+GASGCR+LV Sbjct: 301 LQKAGWTLEQLDLIEANEAFAVQALVVGRELGWDSDRVNVNGGAIALGHPLGASGCRILV 360 Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 SLLHEM +R+A K LATLCIGGGQGVALAL+R Sbjct: 361 SLLHEMQRRNAHKALATLCIGGGQGVALALQR 392 Lambda K H 0.317 0.133 0.376 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: 521 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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