Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012967979.1 KVAR_RS11065 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >NCBI__GCF_000025465.1:WP_012967979.1 Length = 393 Score = 525 bits (1352), Expect = e-154 Identities = 266/393 (67%), Positives = 316/393 (80%), Gaps = 1/393 (0%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 M D+ IVAA RT VGSF+G+ A + A +LGAAV+R LLE+ L A VDE+I GQVLTAG Sbjct: 1 MTDIAIVAAVRTPVGSFRGAFAPLSAVDLGAAVVRSLLERGQLPAAAVDELIFGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 GQNPARQ ++ AGLP P++T+N VCGSGLKA+ QAIRCGDAE++IAGG E+MS Sbjct: 61 CGQNPARQTALRAGLPIDTPAVTVNLVCGSGLKAVQQAVQAIRCGDAEIVIAGGQESMSN 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APY++ AR GLR GHA + DSMI DGLWDAFNDYHMGITAENL D + ISRE QDAFAA Sbjct: 121 APYLMHGARDGLRFGHASLQDSMILDGLWDAFNDYHMGITAENLADAFDISRERQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFK-KD 239 SQ+KA AAI AGRF +EI P+ +PQ K P DEQPR T+ + LA+L+PAF+ D Sbjct: 181 GSQRKAAAAIAAGRFREEIVPVSVPQGKKPPRVVTDDEQPRPETSEQQLAQLRPAFRPAD 240 Query: 240 GSVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRR 299 GSVTAGNASSLNDGAAAVLLM DKA LGLPVLARI S A AGVDP++MGIGPVSA + Sbjct: 241 GSVTAGNASSLNDGAAAVLLMRVDKAHELGLPVLARIVSSAVAGVDPSVMGIGPVSACHK 300 Query: 300 CLDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVL 359 L +AGW+L ++DLIEANEAFA Q+LAVG+ LEWD+EKVNVNGGAIA+GHPIGASGCR+L Sbjct: 301 ALQRAGWTLDEVDLIEANEAFAVQALAVGQLLEWDSEKVNVNGGAIALGHPIGASGCRIL 360 Query: 360 VTLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 V+L+HEM +R A +GLATLC+GGGQG+A+ L+R Sbjct: 361 VSLVHEMQRRGASQGLATLCVGGGQGIAMTLQR 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: 467 Number of extensions: 9 Number of successful extensions: 2 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 WP_012967979.1 KVAR_RS11065 (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.27629.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-153 496.5 2.7 2.9e-153 496.3 2.7 1.0 1 lcl|NCBI__GCF_000025465.1:WP_012967979.1 KVAR_RS11065 acetyl-CoA C-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_012967979.1 KVAR_RS11065 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 496.3 2.7 2.9e-153 2.9e-153 1 384 [. 6 391 .. 6 392 .. 0.99 Alignments for each domain: == domain 1 score: 496.3 bits; conditional E-value: 2.9e-153 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+avRtp+g+++g+++ lsa+dL+aav+++ller +l ++++de+i+G+vl+ag+++n+aR+ al+ag lcl|NCBI__GCF_000025465.1:WP_012967979.1 6 IVAAVRTPVGSFRGAFAPLSAVDLGAAVVRSLLERGQLPAAAVDELIFGQVLTAGCGQNPARQTALRAG 74 8******************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 lp ++pa+tvn vC+Sgl+Av++a+q+i++G+a++v+aGG EsmS++p+l++ + r++l++g+a+l+d lcl|NCBI__GCF_000025465.1:WP_012967979.1 75 LPIDTPAVTVNLVCGSGLKAVQQAVQAIRCGDAEIVIAGGQESMSNAPYLMHGA--RDGLRFGHASLQD 141 *************************************************99997..9************ PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +++ d+ + ++++mg+tAenla+ ++isRe+qD++a+ S++kaa+Ai++g+f +eivpv+v++ lcl|NCBI__GCF_000025465.1:WP_012967979.1 142 SMILDGlwdAFNDYHMGITAENLADAFDISRERQDAFAAGSQRKAAAAIAAGRFREEIVPVSVPQGkkp 210 ****99***99****************************************************988899 PP TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270 ++vv++De++rp+t+ ++La+L+paf++ +gs vtAgN+s+lnDGAaa+llm ++a+elgl +lariv lcl|NCBI__GCF_000025465.1:WP_012967979.1 211 PRVVTDDEQPRPETSEQQLAQLRPAFRPADGS-VTAGNASSLNDGAAAVLLMRVDKAHELGLPVLARIV 278 99*****************************7.************************************ PP TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339 s avagvdp++mg+gpv A +kaL++ag++++++dl+E nEAFA+q+lav + l+ d ekvNvnGGAi lcl|NCBI__GCF_000025465.1:WP_012967979.1 279 SSAVAGVDPSVMGIGPVSACHKALQRAGWTLDEVDLIEANEAFAVQALAVGQLLE-WDSEKVNVNGGAI 346 *******************************************************.88*********** PP TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384 AlGHP+GasG+ri+++l++e+++rg+ GlatlCvggGqG+A+ l lcl|NCBI__GCF_000025465.1:WP_012967979.1 347 ALGHPIGASGCRILVSLVHEMQRRGASQGLATLCVGGGQGIAMTL 391 *******************************************87 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.21 // [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