Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000009985.1:WP_011383284.1 Length = 390 Score = 247 bits (631), Expect = 4e-70 Identities = 150/399 (37%), Positives = 224/399 (56%), Gaps = 25/399 (6%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MT+ VI + RTP+G ++ G+L + A L I A+KRAG++ + V++V++G + Sbjct: 1 MTDIVIAAATRTPVG-SFNGSLAGLQAAQLGEIVIREALKRAGVEAEAVDEVLLGHILTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N AR+A ++AG+P T I++ C SGL+A+AL +++ I V GG ES+ Sbjct: 60 GC-GQNTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESM 118 Query: 121 SLVQND-------KMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEYS 171 S Q+ KM VD ++ D + + M TAE +A+++ I+RE QD ++ Sbjct: 119 SNAQHAIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGITAENLAEKFQITREEQDAFA 178 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSF--KDITLSQDEGPRPETTAEG 229 L SQ + AA + G+F D+I P++ + +K F TL Q P+P +G Sbjct: 179 LGSQNKAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPAFKKDG 238 Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289 T+TA NAS ++DG +A V+M+ K A +G+KPL G + G +P+ Sbjct: 239 ------------TVTAANASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNT 286 Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349 MG GPV A +LL + G +D+ L E NEAFA Q + +G D K+NVNGGAI++G Sbjct: 287 MGYGPVPATQKLLAKLGWKHEDLDLIEANEAFAAQAIAVNKGMGWDTSKVNVNGGAIAIG 346 Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 HP G SGAR+ L E RR AK + T+C+GGGMG A Sbjct: 347 HPIGASGARILVDLLYEMGRRDAKKGLATLCIGGGMGIA 385 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: 418 Number of extensions: 17 Number of successful extensions: 5 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: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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