Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_011427205.1 RHE_RS20545 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000092045.1:WP_011427205.1 Length = 393 Score = 251 bits (642), Expect = 2e-71 Identities = 154/402 (38%), Positives = 225/402 (55%), Gaps = 25/402 (6%) Query: 2 TEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQG 61 + VI S RT +G ++ GA L I+ A+ RAG+D EV++V++G + G Sbjct: 4 SSVVIASAGRTAVG-SFNGAFATVPAHELGAAVIKGALARAGVDAGEVDEVILGQVLAAG 62 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 G N AR+A ++AGLP T +++ C SGL+A+AL + + +I V GG ES+S Sbjct: 63 E-GQNPARQAAIKAGLPKETTAWGVNQLCGSGLRAVALGMQQIATGDAKIIVAGGQESMS 121 Query: 122 LVQND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSL 172 + + KM VD ++ D + M TAE +A+++ +SR+ QD +++ Sbjct: 122 MAPHAVHLRGGVKMGDTKMVDTMIKDGLTDAFHGYHMGITAENIARQWQLSRDEQDRFAV 181 Query: 173 ESQRRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 SQ + AAQ+ G+F DEI P I T+ G D+T+ DE R T E + Sbjct: 182 ASQNKAEAAQKAGRFTDEIIPYVIQTRKG------------DVTVDADEYIRHGATLEAM 229 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 A L+ + T+TA NAS L+DGA+A V+MS+ A +G++PL + G +P M Sbjct: 230 AKLRPAFDKEGTVTAANASGLNDGAAAAVLMSEAEAVRRGIQPLARIVSWATAGVDPSIM 289 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 G GP+ A + L++ G SV+D+ L E NEAFA Q LG DP +NVNGGAI++GH Sbjct: 290 GTGPIPASRKALEKAGWSVNDLDLVEANEAFAAQACAVTKDLGWDPAIVNVNGGAIAIGH 349 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 P G SGAR+ L E +RR AK + T+C+GGGMG A FE Sbjct: 350 PIGASGARVLNTLLFEMKRRGAKKGLATLCIGGGMGVAMCFE 391 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: 436 Number of extensions: 21 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 Apr 09 2024. 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