Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate YP_425366.1 Rru_A0274 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000013085.1:YP_425366.1 Length = 390 Score = 541 bits (1395), Expect = e-159 Identities = 261/390 (66%), Positives = 318/390 (81%) Query: 1 MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60 MT++VI A RT VG+FNG + PAH LG VI V+ RA ++ +V E +LGQ+LTAG Sbjct: 1 MTDIVIAGATRTPVGTFNGGLSGLPAHALGEIVIREVLRRAKVEAGEVDEVVLGQILTAG 60 Query: 61 QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120 QGQNPARQA + AG+P E A+ INQ+CGSGLR VAL Q + LGDA IVVAGGQE+MS+ Sbjct: 61 QGQNPARQAAVNAGIPVEKTAYGINQLCGSGLRTVALGFQAITLGDADIVVAGGQESMSM 120 Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180 +PH +LR+G KMG +D+M+KDGLWDAF+GYHMG TAEN+A KWQISR+ QD F+ Sbjct: 121 APHATYLRSGIKMGTTELVDTMLKDGLWDAFHGYHMGTTAENIAGKWQISREDQDLFSAG 180 Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240 SQNKAEAA AGRF DEIVP +K RKGD+ +D DE+ + G T +++AKLRPAF KDGTV Sbjct: 181 SQNKAEAAIAAGRFKDEIVPVTVKGRKGDIVIDTDEHPKAGVTPESLAKLRPAFSKDGTV 240 Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300 TA NASGINDGAAA+++MS A KRG++PLARI S+ATAG+DP+IMG GPI A+RKALE Sbjct: 241 TAGNASGINDGAAALVLMSEANAAKRGVAPLARIVSWATAGVDPAIMGTGPIPATRKALE 300 Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360 KAGW + DLDL+EANEAFAAQA AVNKD+GWDP+ +NVNGGAIA+GHP+GASGAR+L TL Sbjct: 301 KAGWSIDDLDLIEANEAFAAQALAVNKDLGWDPAKINVNGGAIALGHPVGASGARILVTL 360 Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390 L EM +R+AKKGLATLCIGGGMG+A+C+ER Sbjct: 361 LHEMIKRDAKKGLATLCIGGGMGIALCVER 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: 501 Number of extensions: 14 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 YP_425366.1 Rru_A0274 (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.15338.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-148 478.4 4.6 9.1e-148 478.2 4.6 1.0 1 lcl|NCBI__GCF_000013085.1:YP_425366.1 Rru_A0274 acetyl-CoA acetyltrans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_425366.1 Rru_A0274 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 478.2 4.6 9.1e-148 9.1e-148 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 478.2 bits; conditional E-value: 9.1e-148 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpe 72 i +a+Rtp+g+++g l+ l+a+ L++ vi+e+l+ra++++ ++dev+lG+ l+ag+++n+aR+aa++ag+p lcl|NCBI__GCF_000013085.1:YP_425366.1 6 IAGATRTPVGTFNGGLSGLPAHALGEIVIREVLRRAKVEAGEVDEVVLGQILTAGQGQNPARQAAVNAGIPV 77 7789******************************************************************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144 + a+ +n++C+Sgl++val+ q+i G+ad+vvaGG EsmS +p+ + r+++k+g+++l d++lkd+ lcl|NCBI__GCF_000013085.1:YP_425366.1 78 EKTAYGINQLCGSGLRTVALGFQAITLGDADIVVAGGQESMSMAPHATYL---RSGIKMGTTELVDTMLKDG 146 *********************************************87776...69***************** PP TIGR01930 145 ...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegi 211 + ++++mg+tAen+a k++isRe+qD +++ S++ka++Ai++g+fkdeivpv+vkg+ + v+++De++ lcl|NCBI__GCF_000013085.1:YP_425366.1 147 lwdAFHGYHMGTTAENIAGKWQISREDQDLFSAGSQNKAEAAIAAGRFKDEIVPVTVKGRkgDIVIDTDEHP 218 ***99*******************************************************9999******** PP TIGR01930 212 rpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283 ++++t e+LakL+paf + +g tvtAgN+s++nDGAaal+lmse+ a++ g+ plarivs+a+agvdp++mg lcl|NCBI__GCF_000013085.1:YP_425366.1 219 KAGVTPESLAKLRPAFSK-DG-TVTAGNASGINDGAAALVLMSEANAAKRGVAPLARIVSWATAGVDPAIMG 288 ****************95.9*.6************************************************* PP TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivlt 355 +gp+pA++kaL+kag+si+d+dl+E nEAFAaq+lav+k+lg d++k+NvnGGAiAlGHP+GasGari++t lcl|NCBI__GCF_000013085.1:YP_425366.1 289 TGPIPATRKALEKAGWSIDDLDLIEANEAFAAQALAVNKDLG-WDPAKINVNGGAIALGHPVGASGARILVT 359 ******************************************.88*************************** PP TIGR01930 356 llkeLkergkkyGlatlCvggGqGaAvile 385 ll+e+ +r++k GlatlC+ggG+G+A+ +e lcl|NCBI__GCF_000013085.1:YP_425366.1 360 LLHEMIKRDAKKGLATLCIGGGMGIALCVE 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: 00:00:00.02 # Mc/sec: 7.18 // [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