Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; EC 2.3.1.9 (characterized)
to candidate WP_011428057.1 RHE_RS25075 3-oxoadipyl-CoA thiolase
Query= SwissProt::Q0AVM3 (396 letters) >NCBI__GCF_000092045.1:WP_011428057.1 Length = 401 Score = 336 bits (862), Expect = 6e-97 Identities = 188/399 (47%), Positives = 259/399 (64%), Gaps = 10/399 (2%) Query: 4 EVVLVGACRTPVGTFGGTLKDVGSAQLGAIVMGEAIKRAG-IKAEQIDEVIFGCVLQAGL 62 E + RTP+G F G+L V + LGAI + ++R G + + +D+VIFGC QAG Sbjct: 3 EAFICDYIRTPIGRFAGSLSGVRADDLGAIPLKALMERNGAVDWDAVDDVIFGCANQAGE 62 Query: 63 -GQNVARQCMINAGIPKEVTAFTINKVCGSGLRAVSLAAQVIKAGDADIIMAGGTENMDK 121 +NVAR ++ AG+P V TIN++CGSG+ AV AA+ I+AG+A++++AGG E+M + Sbjct: 63 DNRNVARMSVLLAGLPVAVPGTTINRLCGSGMDAVITAARAIRAGEAELMIAGGVESMSR 122 Query: 122 APFILPNARWGYRMSMPKGDLIDEMVWGGLTDVFNGYH----MGITAENINDMYGITREE 177 APF++P A + + D + W + V + M T EN+ + Y ++RE+ Sbjct: 123 APFVMPKAETAFSRTAEIHDTT--IGWRFINPVMKKQYGVDSMPETGENVAEDYHVSRED 180 Query: 178 QDAFGFRSQTLAAQAIESGRFKDEIVPVVIKGKKGD-IVFDTDEHPRKSTPEAMAKLAPA 236 QDAF RSQ AA A SGR EI PV I +KGD +V D DEHPR +T EA+AKLA Sbjct: 181 QDAFAVRSQAKAAAAQASGRLAKEITPVTIPQRKGDPVVVDRDEHPRATTMEALAKLATP 240 Query: 237 FKK-GGSVTAGNASGINDAAAAVIVMSKEKADELGIKPMAKVVSYASGGVDPSVMGLGPI 295 FKK GG+VTAGNASG+ND AAA+IV S+ A + G+ P+A+++ AS V P VMG+GPI Sbjct: 241 FKKEGGTVTAGNASGVNDGAAALIVASEAAARKYGLTPIARILGGASAAVPPRVMGVGPI 300 Query: 296 PASRKALEKAGLTIDDIDLIEANEAFAAQSIAVARDLGWADKMEKVNVNGGAIAIGHPIG 355 PASRK + + G+ + D+IE NEAFA+Q +AV R LG AD ++VN NGGAIA+GHP+G Sbjct: 301 PASRKLMARLGMNQEQFDVIELNEAFASQGLAVLRALGIADDDQRVNRNGGAIALGHPLG 360 Query: 356 SSGARILVTLLYEMQKRGSKKGLATLCIGGGMGTALIVE 394 SGARI T E+ + K L+T+CIG G G A+ +E Sbjct: 361 MSGARITGTAALELAEARGKYSLSTMCIGVGQGIAIALE 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: 453 Number of extensions: 32 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: 401 Length adjustment: 31 Effective length of query: 365 Effective length of database: 370 Effective search space: 135050 Effective search space used: 135050 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 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