Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_012384743.1 BIND_RS08905 acetyl-CoA C-acyltransferase
Query= reanno::pseudo5_N2C3_1:AO356_21640 (393 letters) >NCBI__GCF_000019845.1:WP_012384743.1 Length = 378 Score = 277 bits (708), Expect = 4e-79 Identities = 171/397 (43%), Positives = 231/397 (58%), Gaps = 27/397 (6%) Query: 1 MQEVVIVAATRTAIG-SFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTA 59 M +VVI R+ + +G LA + +L A V++ L+++TG+ E +++++LG Sbjct: 1 MTKVVIAGYIRSPFTLAKKGELATVRPDDLAAQVVKGLIKKTGIPAEDIEDLLLGCAFPE 60 Query: 60 GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118 G G N AR S LAGLP +V A T+N+ CGS + +H+ A AI+ IA G+E+M Sbjct: 61 GEQGFNVARLVSFLAGLPLSVGASTVNRFCGSSMTTVHMAAGAIQMNAGNAFIAAGVESM 120 Query: 119 SLAPYV----LPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREE 174 S P + LP M A M MG TAEN+ K+ ISR+E Sbjct: 121 SRVPMMGFNPLPNPELAATMPGAYM----------------GMGDTAENVAAKWTISRKE 164 Query: 175 QDAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKP 234 Q+ FA S Q+A AA + GR EI PI RKG TD R TT E L +LKP Sbjct: 165 QEEFALRSHQRATAAQKEGRLTGEIIPIT--GRKG---TITTDGCIRPDTTLEGLAELKP 219 Query: 235 AFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPV 294 AF +G VTAG +S L DGAAAV++ S + AK L VLA + A A +G P IMGIGPV Sbjct: 220 AFSANGVVTAGTSSPLTDGAAAVLVCSEDYAKHHHLDVLASVKAIAVSGCSPEIMGIGPV 279 Query: 295 SATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGAS 354 +A+R+ L +AG Q+D++E NEAFA+QS+A REL D+VN++GGAIALGHP+GA+ Sbjct: 280 AASRKALARAGLEAGQIDIVELNEAFASQSIACMRELNLSPDRVNIDGGAIALGHPLGAT 339 Query: 355 GCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALE 391 G R++ + + K LAT CIGGGQG+A LE Sbjct: 340 GARIVGKAASLLKREKGKYALATQCIGGGQGIATVLE 376 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: 364 Number of extensions: 11 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: 378 Length adjustment: 30 Effective length of query: 363 Effective length of database: 348 Effective search space: 126324 Effective search space used: 126324 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