Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_034994514.1 DL88_RS08065 acetyl-CoA C-acyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000745425.1:WP_034994514.1 Length = 373 Score = 304 bits (779), Expect = 2e-87 Identities = 169/389 (43%), Positives = 231/389 (59%), Gaps = 18/389 (4%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60 M EA IV RTP A +G+LA +RPDDL A + R I+D+ +GCA PE Sbjct: 1 MAEAYIVDYLRTPFAPANRGALAGIRPDDLAASVIAALAARMDFAIEEIEDVNLGCAFPE 60 Query: 61 AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120 EQGLN+AR AGLP ++ +TVNR+C S +Q+I AA I +GA + IAGG ESM Sbjct: 61 GEQGLNIARCAALTAGLPQSIGGVTVNRWCGSSMQAIQMAAGAISMGAGEAFIAGGVESM 120 Query: 121 SQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKAL 180 S+VPMMG PN + E +++MG TAE +A++YG+SRE+QD +++ S + + A Sbjct: 121 SRVPMMGFNPLPNPSWPEGRRLTFVNMGLTAENLAERYGISREEQDDYSLASQKKSLAAR 180 Query: 181 AEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTV 240 A+G+ EI PV V ++G +T L+ L+ F +G+V Sbjct: 181 ADGRLAAEIAPVGAIV------------------EDGCPRETDTTKLAGLKTVFKAEGSV 222 Query: 241 TAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALK 300 TAGNSS +DGA+A ++ + GL PL + SFA+ G PE+MGIGPVEA +ALK Sbjct: 223 TAGNSSPLTDGASATLVCSEDFIKRRGLKPLARVVSFAISGCEPEIMGIGPVEASRKALK 282 Query: 301 LAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSL 360 AG+ D+ + E+NEAFA Q + REL ID ++N +GGAIALGHPLG TG +L Sbjct: 283 RAGITATDLDVIEMNEAFAVQVLACCRELDIDPARLNRDGGAIALGHPLGATGARLAGKA 342 Query: 361 IHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 +KR ++G+ T CIGGG G A V E Sbjct: 343 ASLLKRDQGRYGLATQCIGGGQGIALVLE 371 Lambda K H 0.316 0.133 0.377 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: 416 Number of extensions: 22 Number of successful extensions: 2 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: 373 Length adjustment: 30 Effective length of query: 361 Effective length of database: 343 Effective search space: 123823 Effective search space used: 123823 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_034994514.1 DL88_RS08065 (acetyl-CoA C-acyltransferase)
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.927197.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-133 428.9 0.9 1e-132 428.6 0.9 1.1 1 NCBI__GCF_000745425.1:WP_034994514.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745425.1:WP_034994514.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.6 0.9 1e-132 1e-132 1 385 [] 6 371 .. 6 371 .. 0.95 Alignments for each domain: == domain 1 score: 428.6 bits; conditional E-value: 1e-132 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglp 71 ivd++Rtp++ + +g+l+ ++++dL+a vi +l +r ++ e+i++v lG+++++geq niaR aal+aglp NCBI__GCF_000745425.1:WP_034994514.1 6 IVDYLRTPFApANRGALAGIRPDDLAASVIAALAARMDFAIEEIEDVNLGCAFPEGEQgLNIARCAALTAGLP 78 8*********9779*********************************************************** PP TIGR01930 72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144 +s+ ++tvnr+C+S++qA+++aa +i++G+ ++++aGGvEsmSrvp++ + ++ + + NCBI__GCF_000745425.1:WP_034994514.1 79 QSIGGVTVNRWCGSSMQAIQMAAGAISMGAGEAFIAGGVESMSRVPMMGFNP----LPNPSWPEGRR------ 141 **********************************************988776....44554444455...... PP TIGR01930 145 vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpnttl 217 t ++mg tAenla++ygisReeqD+y+l+S++k+ +A ++g++++ei pv + +D ++ ++t NCBI__GCF_000745425.1:WP_034994514.1 142 -LTFVNMGLTAENLAERYGISREEQDDYSLASQKKSLAARADGRLAAEIAPVGAIV------EDGCP-RETDT 206 .6789**********************************************87653......55555.59999 PP TIGR01930 218 ekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAi 290 kLa+Lk++fk +gs vtAgNss+l+DGA+a+l+ se++ k+ gl+plar+vs+a++g++pe+mg+gpv+A+ NCBI__GCF_000745425.1:WP_034994514.1 207 TKLAGLKTVFKA-EGS-VTAGNSSPLTDGASATLVCSEDFIKRRGLKPLARVVSFAISGCEPEIMGIGPVEAS 277 **********96.8*7.******************************************************** PP TIGR01930 291 ekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLker 363 +kaLk+ag++++d+d++E+nEAFA+qvla+ +el+ +d++++N GGAiAlGHPlGa+Gar+ + ++ Lk++ NCBI__GCF_000745425.1:WP_034994514.1 278 RKALKRAGITATDLDVIEMNEAFAVQVLACCRELD-IDPARLNRDGGAIALGHPLGATGARLAGKAASLLKRD 349 ***********************************.88*********************************** PP TIGR01930 364 gkkyGlatlCvggGqGaAvile 385 +++yGlat C+ggGqG+A++le NCBI__GCF_000745425.1:WP_034994514.1 350 QGRYGLATQCIGGGQGIALVLE 371 ********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (373 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.36 // [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