Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA
Query= reanno::Phaeo:GFF329 (391 letters) >FitnessBrowser__Phaeo:GFF329 Length = 391 Score = 770 bits (1988), Expect = 0.0 Identities = 391/391 (100%), Positives = 391/391 (100%) Query: 1 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA Sbjct: 1 MTNVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAA 60 Query: 61 QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120 QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL Sbjct: 61 QGQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTL 120 Query: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA Sbjct: 121 SPHAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVA 180 Query: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV Sbjct: 181 SQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSV 240 Query: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE Sbjct: 241 TAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALE 300 Query: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL Sbjct: 301 KAGWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTL 360 Query: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP Sbjct: 361 LFEMKRRDAKKGLATLCIGGGMGVAMCVERP 391 Lambda K H 0.316 0.130 0.376 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: 655 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: 391 Length of database: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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 GFF329 PGA1_c03400 (acetyl-CoA acetyltransferase PhaA)
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.29418.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-142 458.7 13.2 8.5e-142 458.5 13.2 1.0 1 lcl|FitnessBrowser__Phaeo:GFF329 PGA1_c03400 acetyl-CoA acetyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.5 13.2 8.5e-142 8.5e-142 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 458.5 bits; conditional E-value: 8.5e-142 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 i +a+Rt++g++gg++++++a+dL+aav+++++erag+d++++ e ilG+vl+a++++n+aR+a ++aglp++ +a+ lcl|FitnessBrowser__Phaeo:GFF329 6 IASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAAQGQNPARQAHINAGLPQESAAW 82 789************************************************************************** PP TIGR01930 78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsm 151 ++n+vC+Sgl+Avalaaq+i+ G+a +v+aGG E+m+ +p+ + r+++k+g+++ d++++d+ + ++++m lcl|FitnessBrowser__Phaeo:GFF329 83 SLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTLSPHAANL---RAGHKMGDMSYIDTMIRDGlwdAFNGYHM 156 ****************************************87765...6999******************99***** PP TIGR01930 152 getAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpa 226 g+tAen+a+k++isRe+qDe+a++S++ka++A+++gkf+dei ++vk++ + +v++De ir + t+e+++kL+pa lcl|FitnessBrowser__Phaeo:GFF329 157 GQTAENVAEKWQISREMQDEFAVASQNKAEAAQKAGKFADEIAAFTVKTRkgDIIVDQDEYIRHGATIEAMQKLRPA 233 ************************************************999999*********************** PP TIGR01930 227 fkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisd 303 f++ +gs vtA+N+s+lnDGAaa+llms + a++ g++plari s+a+ag+dp++mg+gp++A++kaL+kag+s++d lcl|FitnessBrowser__Phaeo:GFF329 234 FAK-DGS-VTAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALEKAGWSVDD 308 *95.9*7.********************************************************************* PP TIGR01930 304 idlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGa 380 +dlvE nEAFAaq+ av+k++g d++ vNvnGGAiA+GHP+GasG+r++ tll e+k+r++k GlatlC+ggG+G+ lcl|FitnessBrowser__Phaeo:GFF329 309 LDLVEANEAFAAQACAVNKDMG-WDPAIVNVNGGAIAIGHPIGASGCRVLNTLLFEMKRRDAKKGLATLCIGGGMGV 384 **********************.88**************************************************** PP TIGR01930 381 Avile 385 A+ +e lcl|FitnessBrowser__Phaeo:GFF329 385 AMCVE 389 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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: 10.23 // [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