Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000009985.1:WP_011383284.1 Length = 390 Score = 500 bits (1288), Expect = e-146 Identities = 253/390 (64%), Positives = 308/390 (78%) Query: 1 MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60 MT++VI +A RT VGSFNG+ A A LG VI + RAG++ V E +LG +LTAG Sbjct: 1 MTDIVIAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKRAGVEAEAVDEVLLGHILTAG 60 Query: 61 QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120 GQN ARQA IKAG+P + A +INQ+CGSGLRAVAL Q ++LGDA+I+VAGGQE+MS Sbjct: 61 CGQNTARQAAIKAGVPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESMSN 120 Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180 + H ++R G KMGD S +D+MIKDGL DAF+ HMG TAEN+A K+QI+R+ QD FA+ Sbjct: 121 AQHAIYMRGGVKMGDASLVDTMIKDGLTDAFSPIHMGITAENLAEKFQITREEQDAFALG 180 Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240 SQNKAEAA KAGRF D+IVP I ++ + D DE+IR G TLD +AK +PAF KDGTV Sbjct: 181 SQNKAEAASKAGRFKDQIVPVTITVKREEKLFDTDEFIRMGCTLDQIAKPKPAFKKDGTV 240 Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300 TAANASGINDG AA+++M+A+EA+KRG+ PLARIA +ATAG DP+ MG GP+ A++K L Sbjct: 241 TAANASGINDGGAALVLMTAKEADKRGIKPLARIAGWATAGTDPNTMGYGPVPATQKLLA 300 Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360 K GWK DLDL+EANEAFAAQA AVNK MGWD S VNVNGGAIAIGHPIGASGAR+L L Sbjct: 301 KLGWKHEDLDLIEANEAFAAQAIAVNKGMGWDTSKVNVNGGAIAIGHPIGASGARILVDL 360 Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390 L+EM RR+AKKGLATLCIGGGMG+A+C+ER Sbjct: 361 LYEMGRRDAKKGLATLCIGGGMGIALCVER 390 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: 457 Number of extensions: 13 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: 390 Length adjustment: 31 Effective length of query: 360 Effective length of database: 359 Effective search space: 129240 Effective search space used: 129240 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 WP_011383284.1 AMB_RS04295 (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.19342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-141 457.2 10.4 2.5e-141 457.0 10.4 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383284.1 AMB_RS04295 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.0 10.4 2.5e-141 2.5e-141 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 457.0 bits; conditional E-value: 2.5e-141 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 i +a+Rtp+g+++gsl+ l+a++L++ vi+e+l+rag+++e++dev lG+ l+ag+++n+aR+aa++ag lcl|NCBI__GCF_000009985.1:WP_011383284.1 6 IAAATRTPVGSFNGSLAGLQAAQLGEIVIREALKRAGVEAEAVDEVLLGHILTAGCGQNTARQAAIKAG 74 789****************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p++ a+++n++C+Sgl+Aval+ q+ik G+a+++vaGG EsmS++ + + ++ ++k+g+a+l d lcl|NCBI__GCF_000009985.1:WP_011383284.1 75 VPNTATAMAINQLCGSGLRAVALGFQAIKLGDANIIVAGGQESMSNAQHAIYMR---GGVKMGDASLVD 140 ************************************************999985...9*********** PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 +++kd+ + + ++mg+tAenla+k++i+ReeqD++al S++ka++A ++g+fkd+ivpv++ k + lcl|NCBI__GCF_000009985.1:WP_011383284.1 141 TMIKDGltdAFSPIHMGITAENLAEKFQITREEQDAFALGSQNKAEAASKAGRFKDQIVPVTITVKreE 209 ******9998889*************************************************999999* PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 k +++De ir + tl+++ak kpafk+ +g tvtA+N+s++nDG aal+lm+ + a++ g++plari + lcl|NCBI__GCF_000009985.1:WP_011383284.1 210 KLFDTDEFIRMGCTLDQIAKPKPAFKK-DG-TVTAANASGINDGGAALVLMTAKEADKRGIKPLARIAG 276 *************************95.9*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+ag dp++mg+gpvpA++k+L+k g++ +d+dl+E nEAFAaq++av+k +g d++kvNvnGGAiA lcl|NCBI__GCF_000009985.1:WP_011383284.1 277 WATAGTDPNTMGYGPVPATQKLLAKLGWKHEDLDLIEANEAFAAQAIAVNKGMG-WDTSKVNVNGGAIA 344 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +GHP+GasGari++ ll+e+ +r++k GlatlC+ggG+G+A+ +e lcl|NCBI__GCF_000009985.1:WP_011383284.1 345 IGHPIGASGARILVDLLYEMGRRDAKKGLATLCIGGGMGIALCVE 389 *****************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (390 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: 00:00:00.01 # Mc/sec: 10.35 // [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