Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_029134160.1 A3GO_RS0115385 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000428045.1:WP_029134160.1 Length = 403 Score = 347 bits (890), Expect = e-100 Identities = 186/400 (46%), Positives = 258/400 (64%), Gaps = 12/400 (3%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKR-AGIKAEQIDEVIFGCVLQAGL 62 + + A RTP+G FGG L V + LGAI + ++R G+ Q+++VIFGC QAG Sbjct: 3 DAYIFDAIRTPIGRFGGALSGVRADDLGAIPLKALMQRNPGVDWSQVEDVIFGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR + AG+P V T+N++CGSG+ AVS+AA+ IK G+A +++AGG E+M + Sbjct: 63 DNRNVARMSALLAGLPAAVPGTTVNRLCGSGMDAVSMAARAIKTGEAQLMIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYHMGI-----TAENINDMYGITRE 176 APF++P A + + ++ D + + GI TAEN+ + + ++R Sbjct: 123 APFVMPKADSAFSR---RAEIHDTTIGWRFVNKLMQQQFGIDSMPETAENVAEQFHVSRA 179 Query: 177 EQDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKG-DIVFDTDEHPRKSTP-EAMAKLA 234 +QDAF RSQ A SGR EIVPV + +KG DIV +DEHPR T E +A L Sbjct: 180 DQDAFALRSQQRTGAAQASGRLAQEIVPVTLLQRKGEDIVVSSDEHPRPDTRLEKLASLP 239 Query: 235 PAFKKGGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGP 294 F+KGGSVTAGNASG+ND A A+++ S+E G+ P A+VV+ + GV+P +MG GP Sbjct: 240 TPFRKGGSVTAGNASGVNDGACALLLGSQEAGKRFGLSPKARVVAATAVGVEPRIMGFGP 299 Query: 295 IPASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPI 354 PASRK L+ GLTI+ +D+IE NEAFAAQ +AV RDLG AD VN NGGAIA+GHP+ Sbjct: 300 APASRKLLQMTGLTIEQMDVIELNEAFAAQGLAVMRDLGLADDAAHVNPNGGAIALGHPL 359 Query: 355 GSSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 G SGAR++ T +Y++Q+ G + L T+CIG G G ALI+E Sbjct: 360 GMSGARLVTTAMYQLQQTGGRYALCTMCIGVGQGIALIIE 399 Lambda K H 0.317 0.135 0.387 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: 480 Number of extensions: 21 Number of successful extensions: 6 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: 396 Length of database: 403 Length adjustment: 31 Effective length of query: 365 Effective length of database: 372 Effective search space: 135780 Effective search space used: 135780 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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