Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_034994454.1 DL88_RS07855 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000745425.1:WP_034994454.1 Length = 391 Score = 577 bits (1488), Expect = e-169 Identities = 285/389 (73%), Positives = 334/389 (85%) Query: 2 TNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQ 61 ++VVIV A RTAVGSFNGAF + PAH+LGAAVI+A + RA + +V E I GQVLTA Sbjct: 3 SDVVIVGAGRTAVGSFNGAFGTVPAHELGAAVIKATLERAKVGPGEVDEVIFGQVLTAAT 62 Query: 62 GQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLS 121 GQNP RQA IKAG+P S AW++NQVCGSGLR+VAL Q + GDA I+VAGGQENMS+S Sbjct: 63 GQNPVRQAAIKAGIPDSSTAWTVNQVCGSGLRSVALGMQQIANGDAKIIVAGGQENMSVS 122 Query: 122 PHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVAS 181 PH A LR+G KMGD+ F+D+M++DGL DAF Y MG TAE++A KWQISR+ QD+FAVAS Sbjct: 123 PHAAFLRSGTKMGDVKFVDTMMRDGLTDAFANYPMGNTAEHIATKWQISREEQDQFAVAS 182 Query: 182 QNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVT 241 QNKAEAAQK GRF +EI+PF + +KGD+ VD DEYIR GAT++AMAKL+PAF+KDGTVT Sbjct: 183 QNKAEAAQKEGRFNEEIIPFTVAGKKGDIIVDKDEYIRLGATIEAMAKLKPAFVKDGTVT 242 Query: 242 AANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEK 301 A N+SGINDGAAA+++MSA+EA+ RGL+PLARIAS+ATAG+DPS+MG GPI ASRKALEK Sbjct: 243 AGNSSGINDGAAAIVLMSADEAKARGLTPLARIASWATAGVDPSLMGSGPIPASRKALEK 302 Query: 302 AGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLL 361 AGWKV DLDLVEANEAFAAQA AVNKDMGWDPSIVNVNGGAIAIGHPIGASGAR+L TLL Sbjct: 303 AGWKVKDLDLVEANEAFAAQAIAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARILVTLL 362 Query: 362 FEMQRRNAKKGLATLCIGGGMGVAMCLER 390 EM RR+AKKG+ATLCIGGGMGVA+ +ER Sbjct: 363 HEMNRRDAKKGIATLCIGGGMGVALTVER 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: 513 Number of extensions: 16 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_034994454.1 DL88_RS07855 (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.18207.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-146 473.5 9.3 2.8e-146 473.3 9.3 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034994454.1 DL88_RS07855 acetyl-CoA C-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034994454.1 DL88_RS07855 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.3 9.3 2.8e-146 2.8e-146 1 385 [] 7 390 .. 7 390 .. 0.98 Alignments for each domain: == domain 1 score: 473.3 bits; conditional E-value: 2.8e-146 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a Rt++g+++g++ +++a++L+aavik+ lera++ p ++devi+G+vl+a++++n+ R+aa++ag lcl|NCBI__GCF_000745425.1:WP_034994454.1 7 IVGAGRTAVGSFNGAFGTVPAHELGAAVIKATLERAKVGPGEVDEVIFGQVLTAATGQNPVRQAAIKAG 75 899****************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p+s a+tvn+vC+Sgl++val++q+i+ G+a+++vaGG E+mS +p+ r++ k+g+ k d lcl|NCBI__GCF_000745425.1:WP_034994454.1 76 IPDSSTAWTVNQVCGSGLRSVALGMQQIANGDAKIIVAGGQENMSVSPHAAF---LRSGTKMGDVKFVD 141 ************************************************7554...47999********* PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 ++++d+ + ++++mg+tAe++a+k++isReeqD++a++S++ka++A++eg+f++ei+p++v gk + lcl|NCBI__GCF_000745425.1:WP_034994454.1 142 TMMRDGltdAFANYPMGNTAEHIATKWQISREEQDQFAVASQNKAEAAQKEGRFNEEIIPFTVAGKkgD 210 ******999899****************************************************99999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 +v+kDe ir + t+e++akLkpaf k+g tvtAgNss++nDGAaa++lms + ak+ gltplari s lcl|NCBI__GCF_000745425.1:WP_034994454.1 211 IIVDKDEYIRLGATIEAMAKLKPAFV-KDG-TVTAGNSSGINDGAAAIVLMSADEAKARGLTPLARIAS 277 9************************9.59*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp+ mg gp+pA++kaL+kag++++d+dlvE nEAFAaq++av+k++g d++ vNvnGGAiA lcl|NCBI__GCF_000745425.1:WP_034994454.1 278 WATAGVDPSLMGSGPIPASRKALEKAGWKVKDLDLVEANEAFAAQAIAVNKDMG-WDPSIVNVNGGAIA 345 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +GHP+GasGari++tll+e+++r++k G+atlC+ggG+G+A+ +e lcl|NCBI__GCF_000745425.1:WP_034994454.1 346 IGHPIGASGARILVTLLHEMNRRDAKKGIATLCIGGGMGVALTVE 390 *****************************************9876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.46 // [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