Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_015931278.1 MNOD_RS27980 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000022085.1:WP_015931278.1 Length = 393 Score = 572 bits (1474), Expect = e-168 Identities = 282/388 (72%), Positives = 330/388 (85%) Query: 3 NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62 ++VIV AART VGSFNGAFA+ PAH+LGA I A + RA + A+V E I GQVLTAG G Sbjct: 6 DIVIVGAARTPVGSFNGAFATLPAHELGAVAIRAALERAKVAPAEVDEVIFGQVLTAGAG 65 Query: 63 QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122 QNPARQA I AG+PQE+ AW +NQ+CGSGLR VA+ Q + GDA I+VAGGQE+MS++P Sbjct: 66 QNPARQAAIAAGIPQEATAWGLNQLCGSGLRTVAIGMQQIANGDAKIIVAGGQESMSMAP 125 Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182 H HLR GQKMGDL+ ID+M+KDGL DAFNGYHMG TAEN+A KWQ++R+ QD FA SQ Sbjct: 126 HAQHLRGGQKMGDLALIDTMLKDGLMDAFNGYHMGNTAENIAQKWQLTREEQDAFATRSQ 185 Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242 NKAEAA+KAGRF EIVP +KTRKG+V V+ADEYIR GAT++AMAKLRPAF K+GTVTA Sbjct: 186 NKAEAARKAGRFKAEIVPVPVKTRKGEVVVEADEYIREGATVEAMAKLRPAFAKEGTVTA 245 Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302 NASGINDGAAA+++M+A EAE+RGL+PLARI S+ATAG+DP IMG GPI ASRKALEKA Sbjct: 246 GNASGINDGAAALVLMAAAEAERRGLTPLARIVSWATAGVDPKIMGTGPIPASRKALEKA 305 Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362 GW ++DL+EANEAFAAQA AVNK++G+D + VNVNGGAIAIGHPIGASGARVL TLL Sbjct: 306 GWSAAEIDLIEANEAFAAQALAVNKELGFDDAKVNVNGGAIAIGHPIGASGARVLVTLLH 365 Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLER 390 EMQRR+AKKGLATLCIGGGMGVAMC+ER Sbjct: 366 EMQRRDAKKGLATLCIGGGMGVAMCVER 393 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: 506 Number of extensions: 15 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 WP_015931278.1 MNOD_RS27980 (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.13200.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-149 482.7 14.9 4.4e-149 482.5 14.9 1.0 1 lcl|NCBI__GCF_000022085.1:WP_015931278.1 MNOD_RS27980 acetyl-CoA C-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000022085.1:WP_015931278.1 MNOD_RS27980 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.5 14.9 4.4e-149 4.4e-149 1 385 [] 9 392 .. 9 392 .. 0.98 Alignments for each domain: == domain 1 score: 482.5 bits; conditional E-value: 4.4e-149 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a+Rtp+g+++g++++l+a++L+a +i+++lera++ p+++devi+G+vl+ag+++n+aR+aa+aag lcl|NCBI__GCF_000022085.1:WP_015931278.1 9 IVGAARTPVGSFNGAFATLPAHELGAVAIRAALERAKVAPAEVDEVIFGQVLTAGAGQNPARQAAIAAG 77 89******************************************************************* PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p++ a+ +n++C+Sgl++va+++q+i+ G+a+++vaGG EsmS +p+ + r + k+g+ l d lcl|NCBI__GCF_000022085.1:WP_015931278.1 78 IPQEATAWGLNQLCGSGLRTVAIGMQQIANGDAKIIVAGGQESMSMAPHAQHL---RGGQKMGDLALID 143 ************************************************75554...699********** PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 ++lkd+ + ++++mg+tAen+a+k++++ReeqD++a rS++ka++A ++g+fk+eivpv vk++ + lcl|NCBI__GCF_000022085.1:WP_015931278.1 144 TMLKDGlmdAFNGYHMGNTAENIAQKWQLTREEQDAFATRSQNKAEAARKAGRFKAEIVPVPVKTRkgE 212 *********99****************************************************999999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 +vv+ De ir++ t+e++akL+paf++ +g tvtAgN+s++nDGAaal+lm + a++ gltplarivs lcl|NCBI__GCF_000022085.1:WP_015931278.1 213 VVVEADEYIREGATVEAMAKLRPAFAK-EG-TVTAGNASGINDGAAALVLMAAAEAERRGLTPLARIVS 279 *************************96.8*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp++mg+gp+pA++kaL+kag+s+ +idl+E nEAFAaq+lav+kelg d++kvNvnGGAiA lcl|NCBI__GCF_000022085.1:WP_015931278.1 280 WATAGVDPKIMGTGPIPASRKALEKAGWSAAEIDLIEANEAFAAQALAVNKELG-FDDAKVNVNGGAIA 347 ******************************************************.78************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +GHP+GasGar+++tll+e+++r++k GlatlC+ggG+G+A+ +e lcl|NCBI__GCF_000022085.1:WP_015931278.1 348 IGHPIGASGARVLVTLLHEMQRRDAKKGLATLCIGGGMGVAMCVE 392 ******************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.98 // [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