Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases
Query= BRENDA::P45359 (392 letters) >FitnessBrowser__Cola:Echvi_1071 Length = 391 Score = 290 bits (743), Expect = 4e-83 Identities = 173/403 (42%), Positives = 248/403 (61%), Gaps = 31/403 (7%) Query: 3 EVVIASAVRTAIGSYGKS-LKDVPAVDLGATAIKEAVKKA-GIKPEDVNEVILGNVL-QA 59 + I RTA+G K + DL IK+ + G++ E V+++I+GN + +A Sbjct: 2 DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61 Query: 60 GLGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMS 119 G R S A L +P IN+ CGSGL ++LA IK+G AD IIAGG E+MS Sbjct: 62 EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120 Query: 120 RAPYLANNARWGYRMG-NAKFVDEMITDGLWDAFNDYH--MGITAENIAERWNISREEQD 176 P + GY+ N K E DY+ MG+TAE +A+ ++ISRE+ D Sbjct: 121 MVPMM------GYKTALNWKIASE---------HPDYYLSMGLTAEELAKDYDISREDSD 165 Query: 177 EFALASQKKAEEAIKSGQFKDEIVPVVIK------GRKGET---VVDTDEHPRFGSTIEG 227 +FA+ S ++A AIK G+FK+EIVP+ ++ K +T VDTDE PR G+ ++ Sbjct: 166 QFAVTSHERAISAIKEGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMDV 225 Query: 228 LAKLKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAI 287 L LKPAFK+ G VTAGN+S +D AA V+MS KEL ++P+A++VSY AGVDP I Sbjct: 226 LGGLKPAFKQGGQVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRI 285 Query: 288 MGYGPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALG 347 MG GP A A+++AG + ++ L+E NEAFAAQ+LAV + L D N VNVNGGA+ALG Sbjct: 286 MGIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALG 345 Query: 348 HPIGASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390 HP+G +GA++ V +++ +++R+ K G+ T C+GGGQG A ++E Sbjct: 346 HPLGCTGAKLTVQMINELRRRNQKYGMVTACVGGGQGVAGVVE 388 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: 429 Number of extensions: 27 Number of successful extensions: 3 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: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 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 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