Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate AO353_01065 AO353_01065 acetyl-CoA acetyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01065 Length = 392 Score = 627 bits (1616), Expect = 0.0 Identities = 315/392 (80%), Positives = 348/392 (88%) Query: 1 MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60 M EVVIVAATRTAIGSFQG+L+AIPA ELGAAVIRRLLEQTG+ Q+DEVILGQVLTAG Sbjct: 1 MNEVVIVAATRTAIGSFQGALSAIPATELGAAVIRRLLEQTGIDAAQIDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQ +I AGLPH PALTLNKVCGSGLKA+HL QAIRCGDAE++IAGG ENMSL Sbjct: 61 AGQNPARQTAIKAGLPHTTPALTLNKVCGSGLKAVHLAVQAIRCGDAELVIAGGQENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180 APYVLP ARTGLRMGHA++ DSMI DGLWDAFNDYHMGITAENL KY ISRE QD FAA Sbjct: 121 APYVLPKARTGLRMGHAQLQDSMIQDGLWDAFNDYHMGITAENLAQKYEISREAQDTFAA 180 Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240 ASQQKA AAIEGGRF EITPILIPQRKG+P+ F TDEQPR +TA++L KLKPAF+KDG Sbjct: 181 ASQQKAAAAIEGGRFQSEITPILIPQRKGEPLVFDTDEQPRIDSTAQALAKLKPAFQKDG 240 Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300 SVTAGNAS+LNDGAA ++L SA KA+ALGLPVLA+I AYA+AGVDP+IMGIGPV ATR Sbjct: 241 SVTAGNASTLNDGAAVLLLASAAKAQALGLPVLARIKAYASAGVDPSIMGIGPVPATRLT 300 Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360 L KAGW++E LDLIEANEAFAAQ+LAV +EL WD KVNVNGGAIALGHPIGASG R+LV Sbjct: 301 LQKAGWNVEDLDLIEANEAFAAQALAVGKELGWDTSKVNVNGGAIALGHPIGASGARILV 360 Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 SL+HE+I+RD KKGLATLCIGGGQGV LA+ER Sbjct: 361 SLVHELIRRDGKKGLATLCIGGGQGVGLAIER 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: 547 Number of extensions: 13 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