Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000009985.1:WP_011383284.1 Length = 390 Score = 308 bits (790), Expect = 1e-88 Identities = 171/400 (42%), Positives = 247/400 (61%), Gaps = 11/400 (2%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M D+ I A RTP+G F G+LAG++A L + ++ ++ V+ + VDEV G A Sbjct: 1 MTDIVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALK-RAGVEAEAVDEVLLGHILTA 59 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 G +N AR A + AG+P + + +N+LC SG+ A+ F+AI G+ + +AGG ESM Sbjct: 60 G-CGQNTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESM 118 Query: 121 SRAPFVMGKAESGYSRN-MKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRA 179 S A + Y R +K+ D ++ I + + M TA+N+A+ +Q++R Sbjct: 119 SNAQHAI------YMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGITAENLAEKFQITRE 172 Query: 180 DQDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKP 239 +QDAFAL SQ KA AA AG F ++IVPV I K+ E + + DE +R TL+ + K KP Sbjct: 173 EQDAFALGSQNKAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKP 232 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 D TVTA NASG+NDG AAL+L +A+ K G+ P AR+ G A+ G P MG GPV Sbjct: 233 AFKKDGTVTAANASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPV 292 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PA +KL +LG D D+IE NEAFA+Q +AV + G+ D +VN NGGAIA+GHP+G Sbjct: 293 PATQKLLAKLGWKHEDLDLIEANEAFAAQAIAVNK--GMGWDTSKVNVNGGAIAIGHPIG 350 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIER 399 SGAR+++ L+++ + +KGLAT+C+G G G+AL +ER Sbjct: 351 ASGARILVDLLYEMGRRDAKKGLATLCIGGGMGIALCVER 390 Lambda K H 0.318 0.134 0.383 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: 391 Number of extensions: 12 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: 400 Length of database: 390 Length adjustment: 31 Effective length of query: 369 Effective length of database: 359 Effective search space: 132471 Effective search space used: 132471 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 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