Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_043530869.1 JH15_RS12340 acetyl-CoA C-acetyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_000759345.1:WP_043530869.1 Length = 393 Score = 597 bits (1540), Expect = e-175 Identities = 296/392 (75%), Positives = 341/392 (86%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60 MQ+VVIVAA RTAIG+F GSLA IPA +LGA VI+ LL +TG+SG+QVDEV+LGQVLTAG Sbjct: 1 MQDVVIVAARRTAIGTFGGSLAGIPASDLGALVIKDLLARTGVSGDQVDEVLLGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 GQNPARQA+I AGLP AVPA+T+NKVCGSGLKALHL QAIRCGDA++IIAGG ENMS+ Sbjct: 61 VGQNPARQAAIKAGLPDAVPAMTINKVCGSGLKALHLATQAIRCGDADLIIAGGQENMSM 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180 +P+VLP +R G RMG K ID+M+ DGLWDAFN+YHMGITAENL +KYGI+R+E D F+A Sbjct: 121 SPHVLPNSRNGQRMGDWKAIDTMVHDGLWDAFNNYHMGITAENLAEKYGITRDEMDEFSA 180 Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240 ASQQKA AAI+ GRF ++ P+ IPQRKGDP+ F DE PRAG TAE LG +KPAFKKDG Sbjct: 181 ASQQKAAAAIDSGRFDSQVVPVEIPQRKGDPIVFDKDEGPRAGVTAEKLGGMKPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300 ++TAGNASS+NDGAAAV++ SAEKAKALGL LA I AYANAGVDP+IMGIGP ATRRC Sbjct: 241 TITAGNASSINDGAAAVMICSAEKAKALGLEPLAYIKAYANAGVDPSIMGIGPAPATRRC 300 Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360 L+KAGWSL++LDL+EANEAFAAQ+LAV +EL WD K+NVNGGAIALGHPIGASGCRV V Sbjct: 301 LEKAGWSLDELDLVEANEAFAAQALAVNKELGWDTSKINVNGGAIALGHPIGASGCRVFV 360 Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 +LLHEMI RD KGLATLCIGGGQGVALA+ER Sbjct: 361 TLLHEMIARDVHKGLATLCIGGGQGVALAIER 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: 555 Number of extensions: 11 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