Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Dsui_3239 Dsui_3239 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__PS:Dsui_3239 Length = 392 Score = 224 bits (572), Expect = 3e-63 Identities = 140/401 (34%), Positives = 213/401 (53%), Gaps = 25/401 (6%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62 E V++S R+ +G + G+L E A L G ++ A+ RAG+DPK V +G + Sbjct: 4 EIVVLSAVRSAVG-GFGGSLAGMEPAELGGLVVKEAIARAGVDPKAVTFATVGNCIPTET 62 Query: 63 TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS- 121 +AR A ++ G+ + + ++R C S +QAI +A++++ + A+GGG E +S Sbjct: 63 RYAYVARLATIQGGMSMDSVAFAVNRLCGSAMQAIVSSAQAIMLGDADYAIGGGVEVMSR 122 Query: 122 -------LVQNDKMNTFHAVDPALEAIKGDVYMAMLD-TAETVAKRYGISRERQDEYSLE 173 L +M A+D + + + + TAE + ++G++RE QD ++LE Sbjct: 123 GAYLLPALRSGARMGDTKAIDAMVSVLTDPFGVGHMGITAENLVTKWGLTREEQDAFALE 182 Query: 174 SQRRTAAAQQGGKFNDEIAPIS--TKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 SQ R A A G+F +I PI+ TK G D+ DE PR TT E LA Sbjct: 183 SQNRAAKAIAEGRFKSQIVPITFQTKKG------------DVVFDTDEHPRA-TTMEALA 229 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 +KA + ++TAGNAS ++D A+ V+ AAA G KP+ G + MG Sbjct: 230 KMKAAFKKDGSVTAGNASGINDAAAFLVLADAAKAAAAGHKPIARLVSYAIAGVPNEIMG 289 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 GP+ + L++ GL++D I L E NEAFA Q L LG+DP K NVNGGAI++GHP Sbjct: 290 EGPIPSSKLALQKAGLTLDQIDLVESNEAFAAQSLAVAKGLGLDPAKTNVNGGAIALGHP 349 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 G +G + L E +R A+Y + TMC+GGG G ++E Sbjct: 350 VGATGGVIVTKLLHEMQRTGARYGMATMCIGGGQGITTIYE 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: 438 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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