Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 3609950 Dshi_3331 acetyl-CoA acetyltransferase (RefSeq)
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Dino:3609950 Length = 394 Score = 248 bits (633), Expect = 2e-70 Identities = 160/401 (39%), Positives = 218/401 (54%), Gaps = 25/401 (6%) Query: 3 EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGA 62 + VI+ ART IG + G+L T TL + A++R+G++ ++ VV G + Sbjct: 6 DIVILDGARTAIG-TFGGSLAGTAPITLGATVAKAALERSGVEGAQIGHVVFGHVINTEP 64 Query: 63 TGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISL 122 ++R A + AG+P TT ++R C SG QA+ +S++ + + GG ES+S Sbjct: 65 RDMYLSRVAAMEAGIPDTTPAMNVNRLCGSGAQALVSVIQSLMLGDAQFGLAGGAESMSR 124 Query: 123 VQ--------NDKMNTFHAVDPALEAIK---GDVYMAMLDTAETVAKRYGISRERQDEYS 171 KM A+D L A+ G +M + TAE VA +GI R QD ++ Sbjct: 125 SPYAMPVARWGQKMGDATAMDMMLGALNCPFGTGHMGV--TAENVAAEHGIGRADQDAFA 182 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 LESQ R A AQ+ G FN +I P+ K V + +DE P+P TTAE LA Sbjct: 183 LESQARAARAQEAGHFNSQIVPVPVK----------VKRDMVDFVRDEHPKP-TTAEALA 231 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 GL+ V + T+TAGNAS ++DGA+A V+ A + GLKP G G P+ MG Sbjct: 232 GLRTVFQKDGTVTAGNASGINDGAAALVLARASAAESAGLKPRARILGYAHAGVRPEVMG 291 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 IGPV AV LL + LSV D + E NEAFA Q L LG+DP K+N NGGAI++GHP Sbjct: 292 IGPVPAVQALLAKTDLSVSDFDVIESNEAFAAQALAVNKGLGLDPAKVNPNGGAIALGHP 351 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 G +GA +A AL E R K A+VTMC+GGG G A FE Sbjct: 352 VGATGAIIALKALYELERIGGKRALVTMCIGGGQGIALAFE 392 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: 466 Number of extensions: 37 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: 394 Length adjustment: 31 Effective length of query: 364 Effective length of database: 363 Effective search space: 132132 Effective search space used: 132132 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