Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_078428592.1 BK574_RS10695 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_002019605.1:WP_078428592.1 Length = 395 Score = 504 bits (1299), Expect = e-147 Identities = 259/390 (66%), Positives = 308/390 (78%) Query: 3 DVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAGSG 62 +VVIVSA RTAVG FGGSL + A LGA VIK+ALE+AGV +QV EVIMG VL AG G Sbjct: 5 EVVIVSAVRTAVGSFGGSLKGVKATTLGATVIKSALEKAGVAGDQVDEVIMGNVLQAGLG 64 Query: 63 QNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSAAP 122 QNPARQAAI+AGLP PAMTINKVCGSGLKAV LA AI++GDA++VVAGG ENMS +P Sbjct: 65 QNPARQAAIEAGLPQYTPAMTINKVCGSGLKAVHLATQAILSGDADVVVAGGMENMSQSP 124 Query: 123 HVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAVGS 182 +V G+RDGFRMGD KL+DTM+ DGL +N YHMG+TAEN+ +Y +TRE QDEFA S Sbjct: 125 YVAMGARDGFRMGDQKLIDTMVFDGLTCAFNDYHMGVTAENLCDQYELTREEQDEFAAWS 184 Query: 183 QNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAGTV 242 Q KA A GKF +EIV V IPQRKGDP+ F TDE+V+ G T + + L+PAF K G+V Sbjct: 185 QEKAAKAIAEGKFKDEIVSVEIPQRKGDPIVFDTDEYVKAGTTAEKLGKLRPAFKKDGSV 244 Query: 243 TAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRALS 302 TA NASGLNDGAAAVVVMS KA ELG+TPLA I+ A+A VDP++MG+GPVPA+K+AL Sbjct: 245 TAGNASGLNDGAAAVVVMSRKKADELGVTPLAVIRGNASAAVDPRIMGIGPVPATKKALE 304 Query: 303 RAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILVTL 362 +A + DL+L+E NEAFAAQALAV + + + +NVNGGAIAIGHPIGASG RILV+L Sbjct: 305 KAGLSLSDLNLIEANEAFAAQALAVGRDLEFPKEILNVNGGAIAIGHPIGASGARILVSL 364 Query: 363 LHEMKRRDAKKGLASLCIGGGMGVALAVER 392 LHE+KRRD + GLA+LCIGGG GVA VE+ Sbjct: 365 LHELKRRDGQYGLATLCIGGGQGVATIVEK 394 Lambda K H 0.315 0.131 0.369 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: 522 Number of extensions: 17 Number of successful extensions: 1 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: 393 Length of database: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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)
Align candidate WP_078428592.1 BK574_RS10695 (acetyl-CoA C-acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01930.hmm # target sequence database: /tmp/gapView.28953.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-156 505.4 6.6 5.6e-156 505.2 6.6 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078428592.1 BK574_RS10695 acetyl-CoA C-acety Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078428592.1 BK574_RS10695 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.2 6.6 5.6e-156 5.6e-156 1 385 [] 8 393 .. 8 393 .. 0.99 Alignments for each domain: == domain 1 score: 505.2 bits; conditional E-value: 5.6e-156 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+avRt++g++ggslk ++a +L+a+vik++le+ag+ +++devi+Gnvlqag ++n+aR+aa++ag lcl|NCBI__GCF_002019605.1:WP_078428592.1 8 IVSAVRTAVGSFGGSLKGVKATTLGATVIKSALEKAGVAGDQVDEVIMGNVLQAGLGQNPARQAAIEAG 76 8******************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 lp+ +pa+t+n+vC+Sgl+Av+la q+i +G+advvvaGG+E+mS++p++ + + r+++++g++kl d lcl|NCBI__GCF_002019605.1:WP_078428592.1 77 LPQYTPAMTINKVCGSGLKAVHLATQAILSGDADVVVAGGMENMSQSPYVAMGA--RDGFRMGDQKLID 143 *************************************************99997..9************ PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +++ d+ + ++++mg+tAenl+++y+++ReeqDe+a+ S++kaakAi+egkfkdeiv ve++++ lcl|NCBI__GCF_002019605.1:WP_078428592.1 144 TMVFDGltcAFNDYHMGVTAENLCDQYELTREEQDEFAAWSQEKAAKAIAEGKFKDEIVSVEIPQRkgd 212 ***9999*999*****************************************************999*9 PP TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270 + v+++De ++++tt+ekL+kL+pafk+ +gs vtAgN+s+lnDGAaa+++ms+++a+elg+tpla i+ lcl|NCBI__GCF_002019605.1:WP_078428592.1 213 PIVFDTDEYVKAGTTAEKLGKLRPAFKK-DGS-VTAGNASGLNDGAAAVVVMSRKKADELGVTPLAVIR 279 9*************************95.9*7.************************************ PP TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339 + a a+vdp++mg+gpvpA++kaL+kagls+sd++l+E nEAFAaq+lav ++l+ +e +NvnGGAi lcl|NCBI__GCF_002019605.1:WP_078428592.1 280 GNASAAVDPRIMGIGPVPATKKALEKAGLSLSDLNLIEANEAFAAQALAVGRDLE-FPKEILNVNGGAI 347 *******************************************************.779********** PP TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 A+GHP+GasGari+++ll+eLk+r+++yGlatlC+ggGqG+A+i+e lcl|NCBI__GCF_002019605.1:WP_078428592.1 348 AIGHPIGASGARILVSLLHELKRRDGQYGLATLCIGGGQGVATIVE 393 ********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (395 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.22 // [ok]
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