Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_011885988.1 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_000016205.1:WP_011885988.1 Length = 399 Score = 363 bits (932), Expect = e-105 Identities = 197/397 (49%), Positives = 271/397 (68%), Gaps = 12/397 (3%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 +++A IV+ +RTP+GKA +G RPD+L +K T+ + G++ I+D IIGCA P Sbjct: 5 LQDAYIVAASRTPIGKAPRGVFKNTRPDELLVHAIKSTIAQVPGFDTKLIEDAIIGCAIP 64 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQGLN+AR LAGLP TV +TVNR+C+SG+ ++A AA++I +G + +AGG ES Sbjct: 65 EAEQGLNVARMGALLAGLPQTVGGVTVNRFCASGITALAMAADRIRVGESEALLAGGCES 124 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177 MS VPMMG+ + + +++ ++ ++ MG TAE+VA+++ VSREDQDAF+V SH+ A Sbjct: 125 MSMVPMMGNKPSMSPHIFDRSEDFGIAYGMGLTAERVAEQWKVSREDQDAFSVESHRKAL 184 Query: 178 KALAEGKFKDEIVPVEVTVT----EIGE-DHKPMEKQFVFSQDEGVRPQTTADILSTLRP 232 A G+F DEI +T GE D K E + DEG R T+ + L+ LR Sbjct: 185 AAQQAGEFGDEIAAYTITERFPNLATGEVDVKTRE----IALDEGPRADTSLEGLAKLRT 240 Query: 233 AFSVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPV 292 F+ G+VTAGNSSQTSDGA A++++ + L PL +F SFAV GVPP++MGIGP Sbjct: 241 VFANKGSVTAGNSSQTSDGAGALLVVSEKVLKEFNLTPLARFVSFAVRGVPPQIMGIGPK 300 Query: 293 EAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCT 352 EAIP ALK AGL+ DI ELNEAFA+Q++ VIR+LG+D KVN GGAIALGHPLG T Sbjct: 301 EAIPAALKAAGLKQDDIDWIELNEAFAAQSLAVIRDLGLDPSKVNPVGGAIALGHPLGAT 360 Query: 353 GTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 G +++H ++RRN ++G+VTMC+G GMGAAG+ E Sbjct: 361 GAIRAATVVHGLRRRNLKYGMVTMCVGTGMGAAGIIE 397 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: 433 Number of extensions: 19 Number of successful extensions: 4 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: 399 Length adjustment: 31 Effective length of query: 360 Effective length of database: 368 Effective search space: 132480 Effective search space used: 132480 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_011885988.1 (acetyl-CoA 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.29691.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-141 458.1 1.6 1.3e-141 458.0 1.6 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011885988.1 acetyl-CoA acetyltransferase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011885988.1 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.0 1.6 1.3e-141 1.3e-141 1 385 [] 10 397 .. 10 397 .. 0.97 Alignments for each domain: == domain 1 score: 458.0 bits; conditional E-value: 1.3e-141 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv+a Rtpig + +g++k++++++Ll+++ik+ ++++ g+d + i+++i+G++++++eq n+aR+ al lcl|NCBI__GCF_000016205.1:WP_011885988.1 10 IVAASRTPIGkAPRGVFKNTRPDELLVHAIKSTIAQVpGFDTKLIEDAIIGCAIPEAEQgLNVARMGAL 78 8*********988******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 aglp++v ++tvnr+CaSg++A+a+aa++i++Ge ++++aGG+EsmS vp++ ++ s++++ ++ lcl|NCBI__GCF_000016205.1:WP_011885988.1 79 LAGLPQTVGGVTVNRFCASGITALAMAADRIRVGESEALLAGGCESMSMVPMMGNKP----SMSPHIFD 143 ***************************************************987775....78888888 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +++ d ++ mg tAe++a+++++sRe+qD+++++Sh+ka +A+++g+f dei +++ ++ lcl|NCBI__GCF_000016205.1:WP_011885988.1 144 RSE----D-FGIAYGMGLTAERVAEQWKVSREDQDAFSVESHRKALAAQQAGEFGDEIAAYTITERfpn 207 777....3.34689**************************************************99*** PP TIGR01930 202 .........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakel 261 ++ ++ Deg+r++t+le LakL+++f++ kgs vtAgNssq++DGA+all++se+v+ke+ lcl|NCBI__GCF_000016205.1:WP_011885988.1 208 latgevdvkTREIALDEGPRADTSLEGLAKLRTVFAN-KGS-VTAGNSSQTSDGAGALLVVSEKVLKEF 274 ******9998899**********************95.8*7.*************************** PP TIGR01930 262 gltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldle 330 +ltplar+vs+av gv+p++mg+gp +Ai++aLk agl+ +did++E+nEAFAaq lav+++lg ld++ lcl|NCBI__GCF_000016205.1:WP_011885988.1 275 NLTPLARFVSFAVRGVPPQIMGIGPKEAIPAALKAAGLKQDDIDWIELNEAFAAQSLAVIRDLG-LDPS 342 ****************************************************************.99** PP TIGR01930 331 kvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 kvN GGAiAlGHPlGa+Ga+ +t+++ L++r+ kyG++t+Cvg+G+GaA i+e lcl|NCBI__GCF_000016205.1:WP_011885988.1 343 KVNPVGGAIALGHPLGATGAIRAATVVHGLRRRNLKYGMVTMCVGTGMGAAGIIE 397 ****************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (399 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: 7.71 // [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