Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_110804635.1 C8J30_RS05090 acetyl-CoA C-acyltransferase family protein
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_003217355.1:WP_110804635.1 Length = 391 Score = 240 bits (613), Expect = 4e-68 Identities = 158/399 (39%), Positives = 216/399 (54%), Gaps = 25/399 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT VI+S ART IG A+ G+L L A A++R+GI P+++ VVMG + Sbjct: 1 MTGIVILSGARTAIG-AFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNT 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 ++R A ++AG+PV T ++R C SG+QAI AA++++ + A+ GG + + Sbjct: 60 EPRDMYVSRVAAIQAGIPVETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVM 119 Query: 121 SLVQ--------NDKMNTFHAVDPALEAIK---GDVYMAMLDTAETVAKRYGISRERQDE 169 S KM +D + A+ G +M + TAE VA ISRE QD Sbjct: 120 SRAPYILPAARFGQKMGDASVIDMMVGALSCPFGTGHMGV--TAENVATECAISREDQDT 177 Query: 170 YSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229 ++LESQ R AAA G F DEI P+ + G V F DE P+ TT + Sbjct: 178 FALESQTRAAAAIAAGAFKDEIVPVE-----IASRKGTVIF-----DTDEHPKA-TTLDK 226 Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289 LA LK +G ++TAGNAS ++DGA A VI + A A GLKPL RG G P+ Sbjct: 227 LAALKPAFLKGGSVTAGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEV 286 Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349 MG+GP+ AV L ++ GL V D + E NEAFA Q L L +DP K+N NGGAI++G Sbjct: 287 MGLGPIPAVRLLCEKTGLKVSDFDVIESNEAFAAQALAVSRALDLDPTKVNPNGGAIALG 346 Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 HP G +GA L L RR + ++TMC+GGG G A Sbjct: 347 HPVGATGAILTVKTLYHLRRTGGRLGLITMCIGGGQGIA 385 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: 454 Number of extensions: 17 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: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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 24 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