Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_028316414.1 G491_RS0124400 acetyl-CoA C-acyltransferase
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_000429905.1:WP_028316414.1 Length = 397 Score = 312 bits (800), Expect = 1e-89 Identities = 187/396 (47%), Positives = 246/396 (62%), Gaps = 16/396 (4%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVK-LKPEQLGDISVG-NVLQP 94 D +V RTP R ++G FKDT P+ LLS +L A + V ++ + D+ +G + + Sbjct: 3 DAYIVSAVRTPGCRRNKGAFKDTRPEALLSHILNAAVDKVPGMEKGDVDDVMMGCSFPEA 62 Query: 95 GAGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154 G + R+A ++G P V +TVNR CSSGL+A+A + + G DI MA GVESMT Sbjct: 63 EQGLNIGRVANQIAGFPIEVSGATVNRFCSSGLEAIALASSRVMVGWSDITMAGGVESMT 122 Query: 155 LSQRGNHGNISSRLLENEKA--RDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAAS 212 G GN+ + +A D MG T+ENVA R+G+SR+ QD FA SQ KA Sbjct: 123 FVPMG--GNMPRPYPNHTQAGGADLYCSMGTTAENVANRYGISREAQDEFAFNSQMKAVK 180 Query: 213 AQSRGCFHAEIVPVTTT--VLNDKGDKKTITVSQD--EGVRPSTTMQGLAKLKPAFKDGG 268 AQ G + EI+P V+ + G K T QD +GVR STT++GLAKL+P F G Sbjct: 181 AQKEGLY-GEIIPTPAVKYVIGEDGLSKQETFLQDFDDGVRESTTLEGLAKLRPVFAAAG 239 Query: 269 STTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAA 328 S TAGNSSQ +DGAAA ++ +K +ELG+ L L Y VG PD MG+GP YAIP Sbjct: 240 SVTAGNSSQTTDGAAACVIMSENKVKELGVKPLAKLVCYTTVGCRPDEMGVGPRYAIPKL 299 Query: 329 LQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIP----AEKVNPLGGAIALGHPLGCTGA 384 L K GLT++DI ++EINEAFASQA+Y + ++G+ EK+N GGAIALGHPLGCTGA Sbjct: 300 LDKVGLTIDDIGLWEINEAFASQALYSIREIGLNKPQYMEKININGGAIALGHPLGCTGA 359 Query: 385 RQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 + TLL + + G + YGV SMCIG GMGAAA+FE Sbjct: 360 KLAATLLYNMNKHGVK-YGVESMCIGGGMGAAALFE 394 Lambda K H 0.317 0.133 0.377 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: 485 Number of extensions: 26 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: 397 Length adjustment: 31 Effective length of query: 393 Effective length of database: 366 Effective search space: 143838 Effective search space used: 143838 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