Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate CCNA_00544 CCNA_00544 acetyl-CoA acetyltransferase
Query= reanno::Phaeo:GFF329 (391 letters) >FitnessBrowser__Caulo:CCNA_00544 Length = 391 Score = 562 bits (1449), Expect = e-165 Identities = 280/389 (71%), Positives = 327/389 (84%) Query: 1 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60 M+ +VI SAART VGSF GA A PA +LG AV++A V RAGI S+V E ILGQVL AA Sbjct: 1 MSEIVIVSAARTPVGSFNGALASLPASELGKAVIEAAVSRAGIAPSDVDEVILGQVLQAA 60 Query: 61 QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120 GQ PARQA + AG+P E+ AWSLNQ+CGSGLRAVALAAQ I G A +V AGGQE+M+ Sbjct: 61 AGQGPARQASVKAGIPVEAPAWSLNQLCGSGLRAVALAAQQIADGSAKVVVAGGQESMSQ 120 Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180 +PHA NLR G KMGD+ ++DTMI+DGLWDAF+GYHMGQTAEN+A +WQI+RE QD+FAV Sbjct: 121 APHAQNLRGGQKMGDLQFVDTMIKDGLWDAFHGYHMGQTAENIASRWQITREDQDKFAVT 180 Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240 SQN+AEAAQKAGKF DEI T+K RKGD IVD+DE+IRHGATIE++Q L+P F K+GSV Sbjct: 181 SQNRAEAAQKAGKFDDEIVPITIKGRKGDTIVDKDEFIRHGATIESVQGLKPVFNKEGSV 240 Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300 TAANASGLNDGAAA +LMSA++A KRG++PLARIAS+A AG++P IMG GPI AS+KALE Sbjct: 241 TAANASGLNDGAAALVLMSAEEAAKRGLKPLARIASWANAGVEPEIMGTGPIPASKKALE 300 Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360 KAGWSV DLDLVE+NEAFAAQA V +++G DPA VNVNGGAIAIGHPIGASG R+L TL Sbjct: 301 KAGWSVSDLDLVESNEAFAAQALCVVRELGLDPAKVNVNGGAIAIGHPIGASGARILTTL 360 Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVE 389 + EMKR AKKGLATLC+GGGMGVAMCVE Sbjct: 361 VHEMKRSGAKKGLATLCVGGGMGVAMCVE 389 Lambda K H 0.316 0.130 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: 499 Number of extensions: 12 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: 391 Length of database: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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 (21.7 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