Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate SMc03879 SMc03879 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >FitnessBrowser__Smeli:SMc03879 Length = 393 Score = 606 bits (1562), Expect = e-178 Identities = 298/388 (76%), Positives = 338/388 (87%) Query: 3 NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62 ++VI SAARTAVGSFNGAF +T AH+LGAA I+AV+ RAG++ +V E ILGQVL AG+G Sbjct: 5 SIVIASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEG 64 Query: 63 QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122 QNPARQA +KAGLPQE AW +NQ+CGSGLRAVAL Q + GDA ++VAGG E+MS++P Sbjct: 65 QNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAP 124 Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182 H AHLR G KMGD ID+MIKDGL DAF GYHMG TAENVA KWQ++R+ QDEFA+ASQ Sbjct: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGITAENVARKWQLTREEQDEFALASQ 184 Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242 NKAEAAQKAGRFADEIVPFV+KTRKGDV VD DEYIRHGATLD++AKLRPAF K+GTVTA Sbjct: 185 NKAEAAQKAGRFADEIVPFVVKTRKGDVNVDQDEYIRHGATLDSIAKLRPAFDKEGTVTA 244 Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302 NASG+NDGAAA L+M+ EA +RG+ PLARI S+ATAG+DP IMG GPI ASRKALEKA Sbjct: 245 GNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 304 Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362 GW V D++LVEANEAFAAQACAVNKD+GWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF Sbjct: 305 GWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 364 Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLER 390 EM+RR KGLATLCIGGGMGVAMC+ER Sbjct: 365 EMKRRGVSKGLATLCIGGGMGVAMCVER 392 Lambda K H 0.317 0.130 0.375 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: 534 Number of extensions: 10 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: 393 Length adjustment: 31 Effective length of query: 360 Effective length of database: 362 Effective search space: 130320 Effective search space used: 130320 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 SMc03879 SMc03879 (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.17531.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-146 474.1 10.5 1.9e-146 473.9 10.5 1.0 1 lcl|FitnessBrowser__Smeli:SMc03879 SMc03879 acetyl-CoA acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc03879 SMc03879 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.9 10.5 1.9e-146 1.9e-146 1 385 [] 8 391 .. 8 391 .. 0.98 Alignments for each domain: == domain 1 score: 473.9 bits; conditional E-value: 1.9e-146 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvp 75 i +a+Rt++g+++g++ ++ a++L+aa+ik++lerag+++ ++devilG+vl+age++n+aR+aa++aglp++ lcl|FitnessBrowser__Smeli:SMc03879 8 IASAARTAVGSFNGAFGNTLAHELGAAAIKAVLERAGVEAGEVDEVILGQVLPAGEGQNPARQAAMKAGLPQEKT 82 789************************************************************************ PP TIGR01930 76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147 a+ +n++C+Sgl+Aval++q+i++G+a+v+vaGG+EsmS +p+ + r ++k+g++k+ d+++kd+ + lcl|FitnessBrowser__Smeli:SMc03879 83 AWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAPHCAHL---RGGVKMGDYKMIDTMIKDGltdAFY 154 ******************************************97776...69*****************999889 PP TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekL 220 +++mg+tAen+a+k++++ReeqDe+al+S++ka++A+++g+f+deivp++vk++ ++ v++De ir + tl+++ lcl|FitnessBrowser__Smeli:SMc03879 155 GYHMGITAENVARKWQLTREEQDEFALASQNKAEAAQKAGRFADEIVPFVVKTRkgDVNVDQDEYIRHGATLDSI 229 9***************************************************99999999*************** PP TIGR01930 221 akLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLk 295 akL+paf++ +g tvtAgN+s+lnDGAaa+llm+e+ a++ g++plarivs+a+agvdp++mg+gp+pA++kaL+ lcl|FitnessBrowser__Smeli:SMc03879 230 AKLRPAFDK-EG-TVTAGNASGLNDGAAAALLMTEAEAARRGIQPLARIVSWATAGVDPQIMGTGPIPASRKALE 302 *******95.8*.6************************************************************* PP TIGR01930 296 kaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGla 370 kag+s+ di+lvE nEAFAaq+ av+k+lg d++ vNvnGGAiA+GHP+GasGar++ tll e+k+rg+ Gla lcl|FitnessBrowser__Smeli:SMc03879 303 KAGWSVADIELVEANEAFAAQACAVNKDLG-WDPSIVNVNGGAIAIGHPIGASGARVLNTLLFEMKRRGVSKGLA 376 ******************************.88****************************************** PP TIGR01930 371 tlCvggGqGaAvile 385 tlC+ggG+G+A+ +e lcl|FitnessBrowser__Smeli:SMc03879 377 TLCIGGGMGVAMCVE 391 ************987 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: 9.38 // [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