Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate H281DRAFT_05723 H281DRAFT_05723 acetyl-CoA acyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >FitnessBrowser__Burk376:H281DRAFT_05723 Length = 400 Score = 317 bits (811), Expect = 5e-91 Identities = 179/399 (44%), Positives = 251/399 (62%), Gaps = 11/399 (2%) Query: 5 EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALER-AAVDPALVGHLVMGNVIPTET 63 + Y+ A RT IG +GG+LKDV DL +KA +ER VD V ++ G Sbjct: 3 DAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRAVDDVIYGCANQAGE 62 Query: 64 RDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSR 123 + ++R++A+ AG+P + P +NRLCGSG+ A+ AA+ + G+A +++ G ESM+R Sbjct: 63 DNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTR 122 Query: 124 GPYLMPAARWGSRMGNAQVIDYMLG------ILHDPFHGIHMGITAENVAARNGITREMQ 177 P++M A + A++ D +G ++ + M TAENVA + GI+R Q Sbjct: 123 APFVMGKAA-SAFARQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQ 181 Query: 178 DALAFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKL-FSVDEHPRATSLEQLAAMKPAF 236 DA A QQ+AA A +G +++I VEI +KG + ++DEHPR TSLE LA +K Sbjct: 182 DAFALVSQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLAKLKGVV 241 Query: 237 KKDGSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPA 296 + DG+VTAGNASG+NDGA AL++AS A L+ AR+V A AGVEP MG+GP PA Sbjct: 242 RPDGTVTAGNASGVNDGACALLIASQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAPA 301 Query: 297 TRLALKRAGLTVADLDVIEANIAFAAQACAVSQELDL--DPAKVNPNGSGIALGHPVGAT 354 T+ L++ G+T+ LDVIE N AFA+Q AV + L L D +VNPNG IALGHP+GA+ Sbjct: 302 TQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGAS 361 Query: 355 GAIIATKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393 GA + T A+H+L R+ GR+AL TMCIG GQGIA + ER+ Sbjct: 362 GARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400 Lambda K H 0.318 0.133 0.378 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: 389 Number of extensions: 18 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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