Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_028316715.1 G491_RS0126720 acetyl-CoA C-acyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_000429905.1:WP_028316715.1 Length = 393 Score = 370 bits (950), Expect = e-107 Identities = 192/391 (49%), Positives = 264/391 (67%), Gaps = 1/391 (0%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M++VVI S RTAIG Y SL + AV+LG TA+ AV+KAGI ++ EV+ G QAG Sbjct: 1 MRDVVIVSGARTAIGGYMGSLSTLSAVELGVTALNGAVEKAGIDKAEIQEVVCGQCNQAG 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 N AR + AGLP E A T+++ C S +R L AQ I G D +A G+E+M+ Sbjct: 61 SPGNTARHIAIGAGLPAESFAFTVHQQCASSMRGAELLAQEIMLGKVDAGVAVGVESMTN 120 Query: 121 APYLANNARWGYRMGNAKFV-DEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFA 179 APYL AR GYR+ + + + D ++ GL DA YHMG+TAENIAER++ISREEQDE+A Sbjct: 121 APYLLMGARKGYRLNDGERIQDSLMIGGLVDALLGYHMGVTAENIAERYDISREEQDEWA 180 Query: 180 LASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDG 239 L S ++A A ++G FKDEI+PV IK RKG DTDEHPR +T+E LA+LKP FKK G Sbjct: 181 LMSHQRAVAATEAGWFKDEILPVEIKTRKGMVTFDTDEHPRADTTLESLARLKPVFKKGG 240 Query: 240 TVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAA 299 TVTAGNASGLND A +V+M+A+KA LG+KPLA++VS V+P +MG G A K A Sbjct: 241 TVTAGNASGLNDAGACIVMMAADKAASLGLKPLARVVSSAPGSVEPEVMGLGVVPAVKNA 300 Query: 300 IEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILV 359 + A + ++D E NEAFAAQ + ++ D++++N G I+LGHP+GA+G R++V Sbjct: 301 LRFAKMDLADMDYFEFNEAFAAQVIGCNREFGLDVDRINAAGSGISLGHPVGATGVRLIV 360 Query: 360 TLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390 T+++ +++R+ + G A+LC GG G A ++E Sbjct: 361 TMINQLRRRNERFGCASLCASGGPGHAFIVE 391 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: 452 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 361 Effective length of database: 362 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 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