Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Ga0059261_2888 Ga0059261_2888 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Korea:Ga0059261_2888 Length = 393 Score = 239 bits (610), Expect = 1e-67 Identities = 160/403 (39%), Positives = 211/403 (52%), Gaps = 24/403 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M++ +I+S RT IG + GAL A L I A+ RAGI V VVMG + Sbjct: 1 MSDVLILSGVRTAIGD-FGGALKNVPAADLGALVIGEAIARAGIAADAVGHVVMGNVIPS 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 + +AR A +RAG+PV T++R C SGLQAI AA+ + +AV GG E++ Sbjct: 60 TPSDAYLARVAAVRAGVPVAVPALTVNRLCGSGLQAIISAAQGIALGECGVAVAGGAENM 119 Query: 121 SLVQN--------DKMNTFHAVDPALEAIKG---DVYMAMLDTAETVAKRYGISRERQDE 169 S + KM +D + V+M + TAE VA + GI R QDE Sbjct: 120 SQAPHYVASARFGQKMGDIQMLDALTRTLSDPFDQVHMGV--TAENVAAQCGIDRAAQDE 177 Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229 ++ES RR A A G+F D+I P+ K G V F DE R E T E Sbjct: 178 AAVESHRRGARAIAEGRFRDQIVPVEIK-----SRGGTVMF-----DTDEHVRAEVTLED 227 Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289 +A L+ T+TAGNAS ++DGA+A V+ S + A G KPL G G EP Sbjct: 228 MARLRPAFQRDGTVTAGNASGINDGAAAVVLGSPEEAQRLGAKPLARILGWGHAGVEPRV 287 Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349 MG+GPV AVP L+R G+++D I + E NEAFA Q +LG DPEK NVNG IS+G Sbjct: 288 MGLGPVEAVPIALRRAGVTLDRIDVIESNEAFAAQACAVSAQLGFDPEKTNVNGSGISLG 347 Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 HP G +GA L E +R + +VTMC+GGG G A + E Sbjct: 348 HPVGATGAINTVKLLYELQRSGGRLGLVTMCIGGGQGIALVIE 390 Lambda K H 0.316 0.134 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: 449 Number of extensions: 28 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: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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