Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_002117405.1:WP_085770214.1 Length = 391 Score = 242 bits (618), Expect = 1e-68 Identities = 154/398 (38%), Positives = 220/398 (55%), Gaps = 25/398 (6%) Query: 2 TEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQG 61 T+ VIVS ART +G ++ GA L A++ A++RA + P EV +V++G + Sbjct: 3 TDIVIVSAARTAVG-SFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLG-A 60 Query: 62 ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121 A G N AR+A ++AG+P + I++ C SGL+A+ALAA+ + +I V GG ES+S Sbjct: 61 AQGQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMS 120 Query: 122 LVQN-------DKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYSL 172 L + KM D + D + M TAE VA ++ ISR QD +++ Sbjct: 121 LSTHAAHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRAEQDAFAV 180 Query: 173 ESQRRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 SQ + AAQ+ GKF DEI P IST+ G D+ + DE + T E + Sbjct: 181 ASQNKAEAAQKAGKFKDEILPYTISTRKG------------DVVVDSDEYVKHGVTLESV 228 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 + L+ + T+TA NAS L+DGA+A V+MS A +GL+PL + G +P M Sbjct: 229 SKLRPAFTKDGTVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIM 288 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 G GP+ A + L++ G V D+ L E NEAFA Q + LG DP +NVNGGAI++GH Sbjct: 289 GSGPIPATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLGWDPAIVNVNGGAIAIGH 348 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SGAR+ L E +RR + T+C+GGGMG A Sbjct: 349 PIGASGARILTTLLYELKRRGGGKGLATLCIGGGMGIA 386 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: 447 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: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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