Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_093394716.1 BM091_RS07565 acetyl-CoA C-acetyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_900114975.1:WP_093394716.1 Length = 392 Score = 538 bits (1386), Expect = e-157 Identities = 259/392 (66%), Positives = 330/392 (84%), Gaps = 1/392 (0%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M VIA+AVRT +GS+GK+L V AVDLG A+KEA+++ + PE V+EVILGNVLQAG Sbjct: 1 MTRAVIATAVRTPVGSFGKTLASVSAVDLGVVALKEALRRINLTPEMVDEVILGNVLQAG 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 GQNPARQ + K+G+P E+PA T+NKVC SGL++V LAAQ I G+A++++AGG+ENMS+ Sbjct: 61 QGQNPARQVAVKSGIPYEVPAFTVNKVCASGLKSVILAAQAIMVGEAEIVVAGGIENMSQ 120 Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180 APY ARWG+RMG+ VD MI DGLWD FN YHMGITAEN+AER+ ISREEQD FAL Sbjct: 121 APYAVPKARWGHRMGDGSLVDLMIFDGLWDIFNGYHMGITAENVAERFGISREEQDRFAL 180 Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVV-DTDEHPRFGSTIEGLAKLKPAFKKDG 239 SQ+KAE AIK G+F++EIVPV + RKG+ ++ DTDEHPRFG+T+E L+KL PAFKK+G Sbjct: 181 RSQQKAEAAIKEGKFREEIVPVTVPQRKGDPIIFDTDEHPRFGTTLEALSKLPPAFKKEG 240 Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299 TVTAGNASG+ND AAV+++MS +KA ELG++P+A+IVSY SAGVDPAIMG GP A++ A Sbjct: 241 TVTAGNASGINDGAAVVIVMSEKKASELGIEPMARIVSYASAGVDPAIMGTGPIPASRKA 300 Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359 +EKAGW+VD+LDLIE+NEAFAAQ++AV +++ +D+ KVNVNGGAIALGHPIGASGARIL Sbjct: 301 LEKAGWSVDDLDLIEANEAFAAQAIAVNREMGWDVEKVNVNGGAIALGHPIGASGARILT 360 Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391 TL++ M++R A++GLATLCIGGGQG A+ +E+ Sbjct: 361 TLLYEMKRRSARRGLATLCIGGGQGCALTVER 392 Lambda K H 0.315 0.132 0.375 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: 538 Number of extensions: 14 Number of successful extensions: 2 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: 392 Length of database: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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