Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_026606572.1 METAC_RS0107670 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000427445.1:WP_026606572.1 Length = 391 Score = 607 bits (1565), Expect = e-178 Identities = 302/388 (77%), Positives = 343/388 (88%) Query: 3 NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62 ++VIVSAARTAVGSFNGAFA+TPAH+LGAA ++A + RA +D ADV E ILGQVL+AGQG Sbjct: 4 DIVIVSAARTAVGSFNGAFAATPAHELGAAAVKAALERAKVDPADVDEVILGQVLSAGQG 63 Query: 63 QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122 QNPARQA IKAG+PQE AW +NQVCGSGLRAVA+ Q + GDA+I+VAGGQE+MS S Sbjct: 64 QNPARQAAIKAGIPQEKTAWGLNQVCGSGLRAVAIGLQQIVNGDANIIVAGGQESMSQSH 123 Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182 H A LRAG KMGD+ F+D+MI+DGL D FN YHMGQTAENVAAKWQISRD QD FA+ASQ Sbjct: 124 HSAFLRAGVKMGDVKFVDTMIRDGLTDVFNNYHMGQTAENVAAKWQISRDEQDRFALASQ 183 Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242 NKAEAAQK G+F +EI PFVI T+KGDVTVDADEYIRHGATL+A+AKL+PAF KDGTVTA Sbjct: 184 NKAEAAQKEGKFKEEITPFVISTKKGDVTVDADEYIRHGATLEALAKLKPAFAKDGTVTA 243 Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302 NASGINDGAAA+++MSA++A RGL+PL RIAS+ATAG+DP++MG GPI ASRKALEKA Sbjct: 244 GNASGINDGAAALVLMSAKDAAARGLAPLGRIASWATAGVDPALMGSGPIPASRKALEKA 303 Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362 GWKV DLDLVEANEAFAAQA AVNKD+GWDPSIVNVNGGAIAIGHPIGASGAR L TLL Sbjct: 304 GWKVKDLDLVEANEAFAAQALAVNKDLGWDPSIVNVNGGAIAIGHPIGASGARALTTLLH 363 Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLER 390 EMQRR AKKGLATLCIGGGMG+A+ +ER Sbjct: 364 EMQRRGAKKGLATLCIGGGMGIALTIER 391 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: 532 Number of extensions: 17 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: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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_026606572.1 METAC_RS0107670 (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.24336.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-147 478.0 11.9 1.2e-147 477.8 11.9 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026606572.1 METAC_RS0107670 acetyl-CoA C-ace Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026606572.1 METAC_RS0107670 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.8 11.9 1.2e-147 1.2e-147 1 385 [] 7 390 .. 7 390 .. 0.98 Alignments for each domain: == domain 1 score: 477.8 bits; conditional E-value: 1.2e-147 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a+Rt++g+++g+++ ++a++L+aa++k++lera++dp+++devilG+vl+ag+++n+aR+aa++ag lcl|NCBI__GCF_000427445.1:WP_026606572.1 7 IVSAARTAVGSFNGAFAATPAHELGAAAVKAALERAKVDPADVDEVILGQVLSAGQGQNPARQAAIKAG 75 8******************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p++ a+ +n+vC+Sgl+Ava++ q+i G+a+++vaGG EsmS++ ++ r+++k+g+ k d lcl|NCBI__GCF_000427445.1:WP_026606572.1 76 IPQEKTAWGLNQVCGSGLRAVAIGLQQIVNGDANIIVAGGQESMSQSHHSA---FLRAGVKMGDVKFVD 141 **********************************************97543...4579*********** PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 ++++d+ v ++++mg+tAen+a+k++isR+eqD++al+S++ka++A++egkfk+ei+p+++ +k + lcl|NCBI__GCF_000427445.1:WP_026606572.1 142 TMIRDGltdVFNNYHMGQTAENVAAKWQISRDEQDRFALASQNKAEAAQKEGKFKEEITPFVISTKkgD 210 *********99****************************************************999999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 ++v+ De ir + tle+LakLkpaf++ +g tvtAgN+s++nDGAaal+lms + a++ gl pl+ri s lcl|NCBI__GCF_000427445.1:WP_026606572.1 211 VTVDADEYIRHGATLEALAKLKPAFAK-DG-TVTAGNASGINDGAAALVLMSAKDAAARGLAPLGRIAS 277 *************************95.9*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp+ mg gp+pA++kaL+kag++++d+dlvE nEAFAaq+lav+k+lg d++ vNvnGGAiA lcl|NCBI__GCF_000427445.1:WP_026606572.1 278 WATAGVDPALMGSGPIPASRKALEKAGWKVKDLDLVEANEAFAAQALAVNKDLG-WDPSIVNVNGGAIA 345 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +GHP+GasGar ++tll+e+++rg+k GlatlC+ggG+G+A+ +e lcl|NCBI__GCF_000427445.1:WP_026606572.1 346 IGHPIGASGARALTTLLHEMQRRGAKKGLATLCIGGGMGIALTIE 390 *****************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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: 11.44 // [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