Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 Length = 393 Score = 241 bits (616), Expect = 2e-68 Identities = 151/398 (37%), Positives = 223/398 (56%), Gaps = 21/398 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M E VIV+ RT IG +++G+L L I + + G+DP +V++V+MG + Sbjct: 1 MQEVVIVAATRTAIG-SFQGSLANVSAVDLGAAVIRQLLAQTGLDPAQVDEVIMGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GA G N AR+A ++AGLP T+++ C SGL+A+ LAA+++ E+ + GG E++ Sbjct: 60 GA-GQNPARQAAIKAGLPFAVPAMTLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENM 118 Query: 121 SLVQ--------NDKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 SL +M VD + D + M TAE +A++Y ++RE+QD + Sbjct: 119 SLSNYVMPGARTGLRMGHAQIVDTMISDGLWDAFNDYHMGITAENLAEKYSLTREQQDAF 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 + SQ++ AA + G+F DEI PI ++ + G ++ + DE PR TTA+ L Sbjct: 179 AAASQQKAVAAIEAGRFADEITPI-----LIPQRKG----DPLSFATDEQPRAGTTADSL 229 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 LKA + ++TAGNAS L+DGA+A ++MS + A A GL L + G +P M Sbjct: 230 GKLKAAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKIAAYANAGVDPAIM 289 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 GIGPV A R L + G S+ + L E NEAFA Q L L D K+NVNGGAI++GH Sbjct: 290 GIGPVSATRRCLDKTGWSIGQLDLIEANEAFAAQSLAVAKDLEWDLNKVNVNGGAIALGH 349 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SG R+ L E ++ AK + T+C+GGG G A Sbjct: 350 PIGASGCRVLVTLLHEMIKQDAKKGLATLCIGGGQGVA 387 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: 385 Number of extensions: 14 Number of successful extensions: 4 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