Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >FitnessBrowser__HerbieS:HSERO_RS20660 Length = 401 Score = 314 bits (805), Expect = 2e-90 Identities = 179/399 (44%), Positives = 251/399 (62%), Gaps = 10/399 (2%) Query: 3 EVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQT-GLSGEQVDEVILGQVLTAGS 61 E +I A RT G + G+L A+ A +L AA IR L+E+ G+ +V++++ G AG Sbjct: 2 EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61 Query: 62 -GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +N AR A +LAGLP AVP T+N++CGS L A+ + A+AI+ G+ +++IAGG+E+M+ Sbjct: 62 DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGISREEQ 175 AP+V+ A + A + D+ I + GI TAEN+ + I+R +Q Sbjct: 122 APFVMGKAESAFARS-AAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180 Query: 176 DAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPA 235 DAFA SQQ+ AA G FA EI P+ IPQ+KGDP+ TDE PR TT +L KLK Sbjct: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240 Query: 236 FKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVS 295 + DG+VTAGNAS +NDGA A++L S + A L A++ A AGV P IMG GP Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300 Query: 296 ATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKW--DMDKVNVNGGAIALGHPIGA 353 A R+ L + G +L Q+D+IE NEAFAAQ LAV R+L D VN NGGAIA+GHP+GA Sbjct: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360 Query: 354 SGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 SG R++ + ++++ + + L T+CIG GQG+AL +ER Sbjct: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399 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: 381 Number of extensions: 16 Number of successful extensions: 5 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: 401 Length adjustment: 31 Effective length of query: 362 Effective length of database: 370 Effective search space: 133940 Effective search space used: 133940 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 17 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