Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_068167432.1 HTA01S_RS04705 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_001592305.1:WP_068167432.1 Length = 401 Score = 369 bits (948), Expect = e-107 Identities = 198/396 (50%), Positives = 271/396 (68%), Gaps = 7/396 (1%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 +++A IV+ RTP+G++ KGS +RPDDL A ++ + + G + ++D+I GCA P Sbjct: 4 IQDAYIVAATRTPIGRSHKGSFKHLRPDDLLAYALRSAMAQVPGLDPKAVEDVICGCAIP 63 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EA+QGLN+AR LAGLP +V ITVNR+C+SGL ++ AA++I +G D IA G ES Sbjct: 64 EAQQGLNVARIGAILAGLPNSVGGITVNRFCASGLSAVQMAADRIRVGEADVMIAAGTES 123 Query: 120 MSQVPMMGHVTRPNLAL---AEKAPEYYMS--MGHTAEQVAKKYGVSREDQDAFAVRSHQ 174 MS VPMMG+ + A+ + +Y ++ MG TAE+VA+++ VSR+ QDAFAV+SHQ Sbjct: 124 MSMVPMMGNAPSLSPAIFANTDDVEKYGIAYGMGLTAEKVAQQWKVSRDAQDAFAVQSHQ 183 Query: 175 NAAKALAEGKFKDEIVPVEVTVTEIG-EDHKPMEKQFVFSQDEGVRPQTTADILSTLRPA 233 A A+ G+F DEI PVEVT + E + + + S DEG RP T+ + L+ LR Sbjct: 184 RAVLAMKNGEFTDEITPVEVTERSVDLETAEVATRSRIISLDEGARPDTSLEGLAKLRTV 243 Query: 234 FSVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVE 293 F+ G+VTAGNSSQTSDGA A++L+ L PL +F S+A GVPP +MGIGPVE Sbjct: 244 FAARGSVTAGNSSQTSDGAGALILVSEAALKRYNLTPLARFVSYASRGVPPHLMGIGPVE 303 Query: 294 AIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTG 353 AIP ALK AGL+ DI FELNEAFA+Q++ V+ LG+D KVN GGAIALGHPLG TG Sbjct: 304 AIPAALKNAGLKQDDIDWFELNEAFAAQSLAVMNTLGLDPAKVNPMGGAIALGHPLGATG 363 Query: 354 TKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 + +++H ++R N+++G+VTMC+G G GAAGVFE Sbjct: 364 AIRSATVVHALRRHNKKYGMVTMCVGMGQGAAGVFE 399 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: 422 Number of extensions: 14 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: 401 Length adjustment: 31 Effective length of query: 360 Effective length of database: 370 Effective search space: 133200 Effective search space used: 133200 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_068167432.1 HTA01S_RS04705 (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.1746.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-146 471.6 4.7 1e-145 471.5 4.7 1.0 1 lcl|NCBI__GCF_001592305.1:WP_068167432.1 HTA01S_RS04705 acetyl-CoA acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001592305.1:WP_068167432.1 HTA01S_RS04705 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.5 4.7 1e-145 1e-145 1 385 [] 9 399 .. 9 399 .. 0.97 Alignments for each domain: == domain 1 score: 471.5 bits; conditional E-value: 1e-145 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv+a+Rtpig + +gs+k+l+++dLla +++++++++ gldp+++++vi+G+++++++q n+aR a+ lcl|NCBI__GCF_001592305.1:WP_068167432.1 9 IVAATRTPIGrSHKGSFKHLRPDDLLAYALRSAMAQVpGLDPKAVEDVICGCAIPEAQQgLNVARIGAI 77 8**********89******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 aglp+sv ++tvnr+CaSgl Av++aa++i++Geadv++a+G EsmS vp++ +a sl++ + lcl|NCBI__GCF_001592305.1:WP_068167432.1 78 LAGLPNSVGGITVNRFCASGLSAVQMAADRIRVGEADVMIAAGTESMSMVPMMGNAP----SLSPAIFA 142 ***************************************************987775....88888888 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 + d ++k + ++ mg tAe++a+++++sR+ qD++a++Shq+a A+++g+f dei+pvev ++ lcl|NCBI__GCF_001592305.1:WP_068167432.1 143 NTDDVEKYG--IAYGMGLTAEKVAQQWKVSRDAQDAFAVQSHQRAVLAMKNGEFTDEITPVEVTERsvd 209 888666655..48***************************************************99*** PP TIGR01930 202 .........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakel 261 ++++s Deg rp+t+le LakL+++f+ gs vtAgNssq++DGA+al+l+se+++k++ lcl|NCBI__GCF_001592305.1:WP_068167432.1 210 letaevatrSRIISLDEGARPDTSLEGLAKLRTVFAA-RGS-VTAGNSSQTSDGAGALILVSEAALKRY 276 *******9999************************96.8*7.*************************** PP TIGR01930 262 gltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldle 330 +ltplar+vs+a gv+p+ mg+gpv+Ai++aLk agl+ +did++E+nEAFAaq lav++ lg ld++ lcl|NCBI__GCF_001592305.1:WP_068167432.1 277 NLTPLARFVSYASRGVPPHLMGIGPVEAIPAALKNAGLKQDDIDWFELNEAFAAQSLAVMNTLG-LDPA 344 ****************************************************************.99** PP TIGR01930 331 kvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 kvN GGAiAlGHPlGa+Ga+ +t++++L++++kkyG++t+Cvg+GqGaA ++e lcl|NCBI__GCF_001592305.1:WP_068167432.1 345 KVNPMGGAIALGHPLGATGAIRSATVVHALRRHNKKYGMVTMCVGMGQGAAGVFE 399 ***************************************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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: 00:00:00.01 # Mc/sec: 9.10 // [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