Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_043827862.1 RSPH17029_RS00115 acetyl-CoA C-acyltransferase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >NCBI__GCF_000015985.1:WP_043827862.1 Length = 389 Score = 488 bits (1255), Expect = e-142 Identities = 252/389 (64%), Positives = 293/389 (75%), Gaps = 2/389 (0%) Query: 5 EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTETR 64 +I V+SA RTAIG FGG+L VP DLATT +AALERA V+P VGH+V G+VI TE R Sbjct: 3 DILVLSAVRTAIGGFGGALAAVPPGDLATTVTRAALERAGVEPGRVGHVVFGHVINTEPR 62 Query: 65 DAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSRG 124 D Y+SRVAAM AGIP E PA NVNRLCGSG+QAI++A Q LMLGDA++ + GAESMSR Sbjct: 63 DMYLSRVAAMQAGIPSEVPAMNVNRLCGSGVQAIVSAMQALMLGDAEVALAGGAESMSRA 122 Query: 125 PYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAFED 184 PY + ARWG +MG+ + +D M G L+ PF HMGITAE VA R+GI+RE QDA A E Sbjct: 123 PYALTTARWGQKMGDTRALDMMTGALNCPFGTGHMGITAEIVAERHGISREDQDAFALES 182 Query: 185 QQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRATSLEQLAAMKPAFKKDGSVTA 244 Q R A A G F QI VEI RKG FS DEHP+AT+LE LA ++PAF+K G+VTA Sbjct: 183 QTRTARAQEEGRFDGQIVPVEIASRKGPVSFSRDEHPKATTLEALAGLRPAFQKGGTVTA 242 Query: 245 GNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLALKRA 304 GNASG+NDGA AL++A AV +PL RL+ YAHAGV+PE MGLGPIPA + R Sbjct: 243 GNASGINDGAGALILAREGAVP--GARPLGRLIGYAHAGVDPEVMGLGPIPAVQALCART 300 Query: 305 GLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIATKAIH 364 GL+VAD DVIE+N AFAAQA AV++ LD DPA+VNPNG IALGHPVGATGAII KA+H Sbjct: 301 GLSVADFDVIESNEAFAAQALAVARALDFDPARVNPNGGAIALGHPVGATGAIITVKALH 360 Query: 365 ELHRTGGRYALVTMCIGGGQGIAAIFERV 393 ELHRTGGR ALVTMCIGGGQGIA ERV Sbjct: 361 ELHRTGGRRALVTMCIGGGQGIALALERV 389 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: 506 Number of extensions: 13 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: 393 Length of database: 389 Length adjustment: 31 Effective length of query: 362 Effective length of database: 358 Effective search space: 129596 Effective search space used: 129596 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 Apr 10 2024. 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