Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AO353_27945 AO353_27945 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_27945 Length = 393 Score = 705 bits (1819), Expect = 0.0 Identities = 360/393 (91%), Positives = 378/393 (96%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 MQDVVIVAATRTA+GSFQGSLASIPAPELGAAVIR+LL +TGL QVDEVILGQVLTAG Sbjct: 1 MQDVVIVAATRTAIGSFQGSLASIPAPELGAAVIRQLLAKTGLAADQVDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 SGQNPARQASILAGLPHAVP+LTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL Sbjct: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYVLPAARTGLRMGHAKM+DSMI+DGLWDAFNDYHMGITAENLVDKY ++RE QDAFAA Sbjct: 121 APYVLPAARTGLRMGHAKMVDSMISDGLWDAFNDYHMGITAENLVDKYHLTREEQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 ASQQKATAAI AGRF DEITPILIPQRKG+P++F VDEQPRA TTAESLAKLKPAFKKDG Sbjct: 181 ASQQKATAAIAAGRFADEITPILIPQRKGEPLSFTVDEQPRAETTAESLAKLKPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASSLNDGAAAVLLMSADKAK LGLPVLA+IA+YANAGVDPAIMGI PVSATRRC Sbjct: 241 SVTAGNASSLNDGAAAVLLMSADKAKQLGLPVLAKIAAYANAGVDPAIMGIAPVSATRRC 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 LDKAGW+L LDLIEANEAFAAQSLAVGKELEWDA KVNVNGGAIA+GHPIGASGCRVLV Sbjct: 301 LDKAGWNLDQLDLIEANEAFAAQSLAVGKELEWDASKVNVNGGAIALGHPIGASGCRVLV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393 +LLHEMIKRDAKKGLATLCIGGGQGVALA+ER+ Sbjct: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALAIERA 393 Lambda K H 0.317 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: 587 Number of extensions: 8 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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)
Align candidate AO353_27945 AO353_27945 (acetyl-CoA 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.4393.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-151 490.6 7.4 1.7e-151 490.5 7.4 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 AO353_27945 acetyl-CoA acetyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 AO353_27945 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 490.5 7.4 1.7e-151 1.7e-151 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 490.5 bits; conditional E-value: 1.7e-151 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaa 65 iv+a+Rt+ig+++gsl++++a +L+aavi++ll+++gl ++++devilG+vl+ag+++n+aR+a lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 6 IVAATRTAIGSFQGSLASIPAPELGAAVIRQLLAKTGLAADQVDEVILGQVLTAGSGQNPARQAS 70 8**************************************************************** PP TIGR01930 66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslk 130 + aglp+ vpalt+n+vC+Sgl+A++l+aq+i++G+a+v++aGG+E+mS +p++l+a+ r +l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 71 ILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYVLPAA--RTGLR 133 ********************************************************98..89*** PP TIGR01930 131 lgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkde 192 +g+ak+ d++++d+ + ++++mg+tAenl +ky+++ReeqD++a++S+qka++Ai++g+f+de lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 134 MGHAKMVDSMISDGlwdAFNDYHMGITAENLVDKYHLTREEQDAFAAASQQKATAAIAAGRFADE 198 *****************99********************************************** PP TIGR01930 193 ivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllms 254 i+p+ ++++ + +++ De++r++tt+e+LakLkpafk+ +gs vtAgN+s+lnDGAaa+llms lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 199 ITPILIPQRkgePLSFTVDEQPRAETTAESLAKLKPAFKK-DGS-VTAGNASSLNDGAAAVLLMS 261 ******999999999***********************95.9*7.******************** PP TIGR01930 255 eevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvla 319 ++ak+lgl +la+i ++a+agvdp++mg++pv A++++L+kag++++++dl+E nEAFAaq la lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 262 ADKAKQLGLPVLAKIAAYANAGVDPAIMGIAPVSATRRCLDKAGWNLDQLDLIEANEAFAAQSLA 326 ***************************************************************** PP TIGR01930 320 vekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384 v kel+ d +kvNvnGGAiAlGHP+GasG+r++++ll+e+ +r++k GlatlC+ggGqG+A+ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 327 VGKELE-WDASKVNVNGGAIALGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALAI 390 ******.88*****************************************************988 PP TIGR01930 385 e 385 e lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 391 E 391 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.45 // [ok]
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