Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate GFF3382 PGA1_c34350 acetyl-CoA acetyltransferase PhbA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >FitnessBrowser__Phaeo:GFF3382 Length = 391 Score = 464 bits (1193), Expect = e-135 Identities = 232/389 (59%), Positives = 290/389 (74%) Query: 5 EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTETR 64 +I ++ ARTAIGTFGGSL DLAT A KAA+ER+ V P +G++V G+VI TE R Sbjct: 3 DIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERSGVAPEQIGNVVFGHVINTEPR 62 Query: 65 DAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSRG 124 D Y+SRVAAM AGIP TPA NVNRLCGSG QAI++ Q+LMLGDA+ + GAE+MSR Sbjct: 63 DMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENMSRS 122 Query: 125 PYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAFED 184 P+++P+ARWG +MG+A+ +D MLG L+ PF HMG+TAENVA + ITR D A Sbjct: 123 PFIVPSARWGQKMGDARALDMMLGALNCPFGTGHMGVTAENVADEHDITRAQMDEFALAS 182 Query: 185 QQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRATSLEQLAAMKPAFKKDGSVTA 244 Q RAA AI GYF+ QI VE++ ++ + F VDEHP+A++LE L +K FKKDG VTA Sbjct: 183 QTRAAAAIEAGYFASQITPVEVKVKRDMVPFDVDEHPKASTLETLGGLKAVFKKDGRVTA 242 Query: 245 GNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLALKRA 304 GNASG+NDGAAA+VMA+ +A + LKP AR++ YAHAGV PE MG+GP+PA + LK+ Sbjct: 243 GNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPVPAVQNLLKKT 302 Query: 305 GLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIATKAIH 364 GL+ +D DV+E+N AFAAQA AV++EL LDPAKVNPNG IALGHPVGATGAII K ++ Sbjct: 303 GLSASDFDVVESNEAFAAQALAVNKELGLDPAKVNPNGGAIALGHPVGATGAIITLKTLY 362 Query: 365 ELHRTGGRYALVTMCIGGGQGIAAIFERV 393 EL R GG L+TMCIGGGQGIA ER+ Sbjct: 363 ELERIGGSKGLITMCIGGGQGIALAIERL 391 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: 487 Number of extensions: 24 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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