Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_057506694.1 ABB28_RS00230 acetyl-CoA acetyltransferase
Query= SwissProt::P07871 (424 letters) >NCBI__GCF_001431535.1:WP_057506694.1 Length = 402 Score = 314 bits (804), Expect = 4e-90 Identities = 188/396 (47%), Positives = 257/396 (64%), Gaps = 14/396 (3%) Query: 37 DVVVVHGRRTPIGRAGRGGFKDTTPDELLSAVLTAVL-QDVKLKPECLGDISVGNVL-QP 94 D +V RTP+G+A +G F++T PD++L+ VL +V+ Q + + D +G + + Sbjct: 7 DAYIVAATRTPVGKAPKGVFRNTRPDDMLAHVLRSVVAQAPGIDVNRIDDAIIGCAMPEA 66 Query: 95 GAGAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G +ARI L+G+P+T+ VNR CSSGLQAVA A IR G+ D+ +A G ESM+ Sbjct: 67 EQGMNVARIGVLLAGLPDTIAAQTVNRFCSSGLQAVAMAADQIRLGNADLMLAGGTESMS 126 Query: 155 LSER-GNPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQKAASA 213 + GN ++ + +N+ MGIT+E VAE + +SR++QDAFALAS QKA +A Sbjct: 127 MVPMMGNKIAMAPSVFDNDHVA-IAYGMGITAEKVAEEWKVSREEQDAFALASHQKAIAA 185 Query: 214 QSKGCFRAEIVP--VTTTVLDDKGDRKTIT----VSQDEGVRPSTTMEGLAKLKPAFKDG 267 G F+ EI P V T D R+ IT V DEG R ++ EGLAKL+P F++G Sbjct: 186 IQNGEFKDEISPYDVRTRQPDLADGRRIITRDKIVDTDEGPRLDSSAEGLAKLRPVFRNG 245 Query: 268 ---GSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYA 324 G+ TAGNSSQ+SDGA AVLLA ++ GL L S++V GV P++MGIGP A Sbjct: 246 QFGGTVTAGNSSQMSDGAGAVLLASEQAVKDYGLKPLARFVSFSVAGVRPEVMGIGPIAA 305 Query: 325 IPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLGCTGA 384 IP AL++AGLT + +D E+NEAFA+Q+L + G+ KVNPLGGAIALGHPLG TGA Sbjct: 306 IPKALKQAGLTQDQLDWIELNEAFAAQSLAVIRDCGLDPSKVNPLGGAIALGHPLGATGA 365 Query: 385 RQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 + TLL+ L+RR ++ YG+V+MCIGTGMGAA +FE Sbjct: 366 IRTATLLHGLRRR-QQKYGMVTMCIGTGMGAAGIFE 400 Lambda K H 0.316 0.133 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: 442 Number of extensions: 16 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: 424 Length of database: 402 Length adjustment: 31 Effective length of query: 393 Effective length of database: 371 Effective search space: 145803 Effective search space used: 145803 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 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