Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_085770214.1 B1812_RS02620 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >NCBI__GCF_002117405.1:WP_085770214.1 Length = 391 Score = 587 bits (1514), Expect = e-172 Identities = 293/389 (75%), Positives = 339/389 (87%) Query: 2 TNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAGQ 61 T++VIVSAARTAVGSFNGAF PAH+LGAA +++ + RA + ++V E ILGQVL A Q Sbjct: 3 TDIVIVSAARTAVGSFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLGAAQ 62 Query: 62 GQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSLS 121 GQNPARQA IKAG+P + A+ INQVCGSGLRAVALAAQ +Q GDA IVVAGGQE+MSLS Sbjct: 63 GQNPARQAAIKAGVPDSATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMSLS 122 Query: 122 PHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVAS 181 H AH+RAG KMG +SF D+MI DGL DAFN YHMG TAENVAAKWQISR QD FAVAS Sbjct: 123 THAAHMRAGTKMGPVSFADTMIIDGLTDAFNNYHMGITAENVAAKWQISRAEQDAFAVAS 182 Query: 182 QNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTVT 241 QNKAEAAQKAG+F DEI+P+ I TRKGDV VD+DEY++HG TL++++KLRPAF KDGTVT Sbjct: 183 QNKAEAAQKAGKFKDEILPYTISTRKGDVVVDSDEYVKHGVTLESVSKLRPAFTKDGTVT 242 Query: 242 AANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALEK 301 AANASG+NDGAAA++VMSA EA+KRGL PLARIA++ATAG+DPSIMG GPI A+RKALEK Sbjct: 243 AANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPIPATRKALEK 302 Query: 302 AGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTLL 361 AGWKV DL+LVEANEAFAAQA AVNKD+GWDP+IVNVNGGAIAIGHPIGASGAR+L TLL Sbjct: 303 AGWKVSDLNLVEANEAFAAQAIAVNKDLGWDPAIVNVNGGAIAIGHPIGASGARILTTLL 362 Query: 362 FEMQRRNAKKGLATLCIGGGMGVAMCLER 390 +E++RR KGLATLCIGGGMG+A+ +ER Sbjct: 363 YELKRRGGGKGLATLCIGGGMGIALAVER 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: 531 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_085770214.1 B1812_RS02620 (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.980008.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-144 465.9 15.2 5.4e-144 465.8 15.2 1.0 1 NCBI__GCF_002117405.1:WP_085770214.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002117405.1:WP_085770214.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.8 15.2 5.4e-144 5.4e-144 1 385 [] 7 390 .. 7 390 .. 0.98 Alignments for each domain: == domain 1 score: 465.8 bits; conditional E-value: 5.4e-144 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+a+Rt++g+++g++ ++a++L+aa++k++lera++ p+++ evilG+vl a++++n+aR+aa++ag+p+s NCBI__GCF_002117405.1:WP_085770214.1 7 IVSAARTAVGSFNGAFGGVPAHELGAAAVKSALERAKVAPSEVCEVILGQVLGAAQGQNPARQAAIKAGVPDS 79 8************************************************************************ PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 a+ +n+vC+Sgl+Avalaaq+i+aG+a++vvaGG EsmS + + ++ r++ k+g + +d+++ d+ NCBI__GCF_002117405.1:WP_085770214.1 80 ATAFGINQVCGSGLRAVALAAQQIQAGDAQIVVAGGQESMSLSTHAAHM---RAGTKMGPVSFADTMIIDGlt 149 ******************************************9987777...588999999999999999999 PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 + ++++mg+tAen+a+k++isR eqD++a++S++ka++A+++gkfkdei+p+++ ++ ++vv++De ++ + NCBI__GCF_002117405.1:WP_085770214.1 150 dAFNNYHMGITAENVAAKWQISRAEQDAFAVASQNKAEAAQKAGKFKDEILPYTISTRkgDVVVDSDEYVKHG 222 999****************************************************999999************ PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 +tle+++kL+paf++ +g tvtA+N+s+lnDGAaal++ms + ak+ gl+plari ++a+agvdp++mg gp+ NCBI__GCF_002117405.1:WP_085770214.1 223 VTLESVSKLRPAFTK-DG-TVTAANASGLNDGAAALVVMSAAEAKKRGLEPLARIAAWATAGVDPSIMGSGPI 293 *************95.9*.6***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 pA++kaL+kag+++sd++lvE nEAFAaq++av+k+lg d++ vNvnGGAiA+GHP+GasGari++tll+eL NCBI__GCF_002117405.1:WP_085770214.1 294 PATRKALEKAGWKVSDLNLVEANEAFAAQAIAVNKDLG-WDPAIVNVNGGAIAIGHPIGASGARILTTLLYEL 365 **************************************.88******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 k+rg+ GlatlC+ggG+G+A+ +e NCBI__GCF_002117405.1:WP_085770214.1 366 KRRGGGKGLATLCIGGGMGIALAVE 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: 00:00:00.00 # Mc/sec: 25.58 // [ok]
This GapMind analysis is from Apr 09 2024. 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