Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Putida:PP_4636 Length = 392 Score = 251 bits (642), Expect = 2e-71 Identities = 153/398 (38%), Positives = 226/398 (56%), Gaps = 21/398 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M + VIV+ RT IG +++GAL L I+ +K+ G+DP +V++V++G + Sbjct: 1 MNDVVIVAATRTAIG-SFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GA G N AR+A ++AGLP + T+++ C SGL+A+ LAA+++ E+ + GG E++ Sbjct: 60 GA-GQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENM 118 Query: 121 SLVQ--------NDKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 SL +M +D + D + M TAE + +YG+SRE+QD + Sbjct: 119 SLAPYVMPSARTGQRMGHGQLIDSMITDGLWDAFNDYHMGITAENLVDKYGLSREQQDAF 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 + ESQR+ AA + G+F+ EI PI V+ + G ++DE PRP+TTAE L Sbjct: 179 AAESQRKAVAAIEAGRFDAEITPI-----VLPQKKGEPK----VFARDEQPRPDTTAESL 229 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 A L+ + ++TAGNAS L+DGA+A ++MS A A GL L S G +P M Sbjct: 230 AKLRPAFKKDGSVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIM 289 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 GIGPV A R L + G + ++ L E NEAFA Q L + L D ++NVNGGAI++GH Sbjct: 290 GIGPVSATQRCLDKAGWQLAELDLIEANEAFAAQALAVGNALAWDAARVNVNGGAIALGH 349 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SG R+ L E +R K + T+C+GGG G A Sbjct: 350 PIGASGCRVLVTLLHEMIKRDVKKGLATLCIGGGQGVA 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: 412 Number of extensions: 17 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: 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