Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000018545.1:WP_012709751.1 Length = 393 Score = 252 bits (644), Expect = 1e-71 Identities = 150/395 (37%), Positives = 224/395 (56%), Gaps = 25/395 (6%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VI S ART +G ++ GA T L I+ ++RAG+D EV++V++G + G G Sbjct: 7 VIASAARTAVG-SFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGE-G 64 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124 N AR+A ++AG+P +++ C SGL+A+AL + + I V GG ES+S+ Sbjct: 65 QNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAP 124 Query: 125 ND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQ 175 + KM + +D ++ D + M TAE VA+++ ++RE QDE++L SQ Sbjct: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGTTAENVARKWQLTREEQDEFALRSQ 184 Query: 176 RRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233 + AAQ+ G+F DEI P + T+ G D+T+ QDE R T E +A L Sbjct: 185 NKAEAAQKAGRFADEIVPFIVKTRKG------------DVTVDQDEYIRHGATLESIAKL 232 Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293 + + T+TAGNAS L+DGA+AT++M++ AA +G++PL + G +P MG G Sbjct: 233 RPAFDKEGTVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTG 292 Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353 P+ A + L++ G + D+ L E NEAFA Q LG DP +NVNGGAI++GHP G Sbjct: 293 PIPASRKALEKAGWPIGDVELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIG 352 Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 SGAR+ L E +RR + T+C+GGGMG A Sbjct: 353 ASGARVLNTLLFEMKRRGVSKGLATLCIGGGMGVA 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: 427 Number of extensions: 21 Number of successful extensions: 4 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: 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