Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_100847720.1 C0J26_RS26305 thiolase family protein
Query= BRENDA::Q8VCH0 (424 letters) >NCBI__GCF_003031005.1:WP_100847720.1 Length = 394 Score = 278 bits (712), Expect = 2e-79 Identities = 168/390 (43%), Positives = 235/390 (60%), Gaps = 7/390 (1%) Query: 37 DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPGA 96 +VV+V RT + ++ RG F T PD++ + + A+L + P + D VG GA Sbjct: 3 EVVIVDSVRTGLAKSFRGKFNQTRPDDMAAHCVNALLSRNDIDPASVEDCIVGAGSNEGA 62 Query: 97 -GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155 G + R LS + V T+NR CSSGLQA+A A I +G DI +A GVES++L Sbjct: 63 QGYNIGRNVAVLSQLGTGVAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESISL 122 Query: 156 SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQS 215 + + + + L ++ MG T+E VA R+GVSR+ QD ++L SQ + A AQ+ Sbjct: 123 TLKSVNTDHLINPLLKQQTPGIYYTMGQTAEVVARRYGVSREAQDRYSLQSQLRTAQAQA 182 Query: 216 RGCFHAEIVPVTTTV-LNDK--GDKKTIT--VSQDEGVRPSTTMQGLAKLKPAFKDGGST 270 G F EIVP+ + DK G+ + + V +D+ RP TT + LA LKP F D GS Sbjct: 183 AGLFDDEIVPMAVKYRVEDKNSGEVQILDGIVERDDCNRPDTTYESLAGLKPVFADDGSV 242 Query: 271 TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQ 330 TAGNSSQ+SDGA+ L+ KA +LGL R + V G PD MGIGP +++P L+ Sbjct: 243 TAGNSSQLSDGASMTLVMSLEKALQLGLKPKAFFRGFTVAGCAPDEMGIGPVFSVPKLLK 302 Query: 331 KAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTL 390 GL V DID++E+NEAFASQ +Y ++L I +K N GG+I++GHP G TG+RQV L Sbjct: 303 AKGLQVADIDLWELNEAFASQCLYARDRLEIDNDKYNVNGGSISIGHPFGMTGSRQVGHL 362 Query: 391 LNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420 + EL+RR R YG+V+MC+G GMGA +FE Sbjct: 363 VRELQRRNLR-YGIVTMCVGGGMGATGLFE 391 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: 422 Number of extensions: 17 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 424 Length of database: 394 Length adjustment: 31 Effective length of query: 393 Effective length of database: 363 Effective search space: 142659 Effective search space used: 142659 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