Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate PP_3754 PP_3754 Beta-ketothiolase BktB
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411 (393 letters) >FitnessBrowser__Putida:PP_3754 Length = 394 Score = 563 bits (1451), Expect = e-165 Identities = 284/394 (72%), Positives = 328/394 (83%), Gaps = 1/394 (0%) Query: 1 MNTPEIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIP 60 M++ EIYVVSA R+AIG FGGSLKD+PLADLA+ +AA+ER+ + VGH+VMG VIP Sbjct: 1 MSSAEIYVVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSGLAAEQVGHMVMGTVIP 60 Query: 61 TETRDAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAES 120 TE RDAY++RVAAMNAGIPKETPA+NVNRLCGSGLQAI++AAQ L+LGD D+ V AGAES Sbjct: 61 TEPRDAYLARVAAMNAGIPKETPAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAES 120 Query: 121 MSRGPYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDAL 180 MSRGPYL+P ARWG+RMG+ Q IDY +G+L DPF HMGITAENV+A+ GITREMQD L Sbjct: 121 MSRGPYLLPQARWGARMGDLQGIDYTVGVLQDPFQHFHMGITAENVSAKYGITREMQDEL 180 Query: 181 AFEDQQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRA-TSLEQLAAMKPAFKKD 239 A Q+RAA AIA G F+ QI +E++ RKG FSVDEH RA + EQLA MKP FKKD Sbjct: 181 ALTSQRRAARAIAEGRFASQIVALELKTRKGSVQFSVDEHVRADVTAEQLAGMKPVFKKD 240 Query: 240 GSVTAGNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRL 299 G+VTAGNASG+NDGAA LV+A+G+AV+ LKPLARLV YAHAGVEPE MGLGPIPATR Sbjct: 241 GTVTAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPIPATRK 300 Query: 300 ALKRAGLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIA 359 L++ GL + DLDVIE+N AFAAQACAV++EL DP KVNPNGSGI+LGHPVGATGAIIA Sbjct: 301 VLEKTGLNLQDLDVIESNEAFAAQACAVARELGFDPEKVNPNGSGISLGHPVGATGAIIA 360 Query: 360 TKAIHELHRTGGRYALVTMCIGGGQGIAAIFERV 393 TKAIHEL R GRYAL TMCIGGGQGIA +FERV Sbjct: 361 TKAIHELQRIQGRYALATMCIGGGQGIAVVFERV 394 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: 520 Number of extensions: 23 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: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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