Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_012168837.1 AZC_RS01555 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_000010525.1:WP_012168837.1 Length = 392 Score = 568 bits (1463), Expect = e-166 Identities = 283/389 (72%), Positives = 329/389 (84%) Query: 3 NVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQG 62 +VVIVSAART VGSFNGA ++ PAH LGA I+A + RAG+ ++VSE ILGQVLTA QG Sbjct: 4 DVVIVSAARTPVGSFNGALSTLPAHQLGAIAIKAALERAGVAASEVSEVILGQVLTAAQG 63 Query: 63 QNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLSP 122 QNPARQA I AG+P ES AW +NQVCGSGLR+VAL Q ++ GD+S+VVAGGQE+MS S Sbjct: 64 QNPARQASIAAGVPIESPAWQVNQVCGSGLRSVALGYQAIKNGDSSLVVAGGQESMSQST 123 Query: 123 HVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVASQ 182 H AHLR G +MG L +D+MIKDGLWDAFNGYHMG TAENVA ++QI+R QDEFAVASQ Sbjct: 124 HAAHLRNGTRMGSLDLVDTMIKDGLWDAFNGYHMGNTAENVATQFQITRAEQDEFAVASQ 183 Query: 183 NKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVTA 242 +KAEAAQKAGRF +EIVP I +RKGDV VD DEY RHGAT++AM KL+PAF+KDGTVTA Sbjct: 184 HKAEAAQKAGRFKEEIVPVTISSRKGDVVVDTDEYPRHGATIEAMQKLKPAFVKDGTVTA 243 Query: 243 ANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEKA 302 ANASGINDG AAV++MSAE A K G +PLARI S+A AG+DP++MG GPI AS+ ALEKA Sbjct: 244 ANASGINDGGAAVVLMSAERAAKEGKTPLARIVSWAQAGVDPAVMGTGPIPASKLALEKA 303 Query: 303 GWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLLF 362 GW V DLDL+EANEAFAAQA AVNK +GWD + VNVNGGAIAIGHPIGASG R+L TLL Sbjct: 304 GWTVDDLDLIEANEAFAAQAIAVNKGLGWDTAKVNVNGGAIAIGHPIGASGTRILVTLLH 363 Query: 363 EMQRRNAKKGLATLCIGGGMGVAMCLERP 391 EMQ+R+AKKGLATLCIGGGMG+A+C+ERP Sbjct: 364 EMQKRDAKKGLATLCIGGGMGIALCVERP 392 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: 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: 392 Length adjustment: 31 Effective length of query: 360 Effective length of database: 361 Effective search space: 129960 Effective search space used: 129960 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_012168837.1 AZC_RS01555 (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.7511.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-146 471.7 12.3 9.8e-146 471.5 12.3 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012168837.1 AZC_RS01555 acetyl-CoA C-acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012168837.1 AZC_RS01555 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.5 12.3 9.8e-146 9.8e-146 1 385 [] 7 390 .. 7 390 .. 0.98 Alignments for each domain: == domain 1 score: 471.5 bits; conditional E-value: 9.8e-146 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a+Rtp+g+++g+l++l+a++L+a +ik++lerag+ ++++ evilG+vl+a++++n+aR+a +aag lcl|NCBI__GCF_000010525.1:WP_012168837.1 7 IVSAARTPVGSFNGALSTLPAHQLGAIAIKAALERAGVAASEVSEVILGQVLTAAQGQNPARQASIAAG 75 8******************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p + pa++vn+vC+Sgl++val++q+ik G+ ++vvaGG EsmS++ + + r++ ++g+ +l d lcl|NCBI__GCF_000010525.1:WP_012168837.1 76 VPIESPAWQVNQVCGSGLRSVALGYQAIKNGDSSLVVAGGQESMSQSTHAAHL---RNGTRMGSLDLVD 141 ***********************************************865554...79*********** PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 +++kd+ + ++++mg+tAen+a++++i+R eqDe+a++S++ka++A+++g+fk+eivpv++ + + lcl|NCBI__GCF_000010525.1:WP_012168837.1 142 TMIKDGlwdAFNGYHMGNTAENVATQFQITRAEQDEFAVASQHKAEAAQKAGRFKEEIVPVTISSRkgD 210 *********99****************************************************999999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 +vv++De +r + t+e+++kLkpaf k+g tvtA+N+s++nDG aa++lms e+a++ g tplarivs lcl|NCBI__GCF_000010525.1:WP_012168837.1 211 VVVDTDEYPRHGATIEAMQKLKPAFV-KDG-TVTAANASGINDGGAAVVLMSAERAAKEGKTPLARIVS 277 *************************9.59*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp++mg+gp+pA++ aL+kag++++d+dl+E nEAFAaq++av+k lg d++kvNvnGGAiA lcl|NCBI__GCF_000010525.1:WP_012168837.1 278 WAQAGVDPAVMGTGPIPASKLALEKAGWTVDDLDLIEANEAFAAQAIAVNKGLG-WDTAKVNVNGGAIA 345 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +GHP+GasG+ri++tll+e+++r++k GlatlC+ggG+G+A+ +e lcl|NCBI__GCF_000010525.1:WP_012168837.1 346 IGHPIGASGTRILVTLLHEMQKRDAKKGLATLCIGGGMGIALCVE 390 *****************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 8.30 // [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