Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >FitnessBrowser__Pedo557:CA265_RS17585 Length = 391 Score = 388 bits (996), Expect = e-112 Identities = 199/389 (51%), Positives = 264/389 (67%), Gaps = 1/389 (0%) Query: 3 EAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATPEA 61 EA I++G RT VGKA +G R DDL A ++ + + IDD+I+G ATPEA Sbjct: 2 EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61 Query: 62 EQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESMS 121 EQGLN+ R I + VP +TVNRYC+SGL +IA A KI G D IAGG E MS Sbjct: 62 EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121 Query: 122 QVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKALA 181 +P G PN +A+ P++Y MG TAE VAK+Y VSREDQDAF+++SH+ A A+ Sbjct: 122 GMPFGGWKLVPNAEVAKNNPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAIHAIK 181 Query: 182 EGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTVT 241 G KD I+P+ V + + K + +V DEG R TT D L+ L+P F G+VT Sbjct: 182 NGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTLDKLAKLKPVFDAVGSVT 241 Query: 242 AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALKL 301 AGNSSQTSDGAA V+++ +K L P+ + S+ + GVPP +MGIGP+EAIP+ALK Sbjct: 242 AGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPPRIMGIGPIEAIPKALKQ 301 Query: 302 AGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSLI 361 AGL+ +DI L ELNEAFASQ++ VIR L ++ + +NVNGGAIALGHPLGCTG KLT+ ++ Sbjct: 302 AGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPLGCTGAKLTVQIM 361 Query: 362 HEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390 +E+KR+N+++G+VTMC+G G GAAG+FEL Sbjct: 362 NELKRQNKKYGMVTMCVGTGQGAAGIFEL 390 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: 404 Number of extensions: 14 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: 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate CA265_RS17585 CA265_RS17585 (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.17834.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-138 447.6 0.5 2.1e-138 447.4 0.5 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS17585 CA265_RS17585 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.4 0.5 2.1e-138 2.1e-138 1 385 [] 5 389 .. 5 389 .. 0.95 Alignments for each domain: == domain 1 score: 447.4 bits; conditional E-value: 2.1e-138 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaa 65 i++++Rt++g + +g+++ ++a+dL+a+vi++l++ + +ld+e+id+vi+Gn+++++eq ni+R++ lcl|FitnessBrowser__Pedo557:CA265_RS17585 5 IIAGYRTAVGkAPRGVFRFTRADDLAAEVIRALVASVpNLDNEQIDDVIVGNATPEAEQgLNIGRMIS 72 89********988******************************************************9 PP TIGR01930 66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgk 133 l ++vp++tvnr+CaSgl+++a+a++kikaG+ad+++aGGvE mS +p++ +l +++ lcl|FitnessBrowser__Pedo557:CA265_RS17585 73 LMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMSGMPFGGW------KLVPNA 134 98777899********************************************8544......455533 PP TIGR01930 134 akledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201 ++ ++ mg tAe +ak+y++sRe+qD+++l+Sh+ka +Ai++g++kd i+p++v+++ lcl|FitnessBrowser__Pedo557:CA265_RS17585 135 EVAKN-----NPDWYWGMGLTAEAVAKEYNVSREDQDAFSLKSHEKAIHAIKNGHLKDGILPITVNEN 197 32222.....457789**************************************************99 PP TIGR01930 202 ...........kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseeva 258 + vv++Deg+r++ttl+kLakLkp+f+ gs vtAgNssq++DGAa++l++se+++ lcl|FitnessBrowser__Pedo557:CA265_RS17585 198 yldanlkkktrSYVVDTDEGPRADTTLDKLAKLKPVFDA-VGS-VTAGNSSQTSDGAAFVLVVSEKKM 263 *******99998999**********************96.797.************************ PP TIGR01930 259 kelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgs 326 kel+ +p+ar+vs+++agv+p++mg+gp++Ai+kaLk+agl+ +didl+E+nEAFA+q lav++ l+ lcl|FitnessBrowser__Pedo557:CA265_RS17585 264 KELNAEPIARLVSYGIAGVPPRIMGIGPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLD- 330 *******************************************************************. PP TIGR01930 327 ldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 l+++ +NvnGGAiAlGHPlG++Ga +++++++eLk+++kkyG++t+Cvg+GqGaA i+e lcl|FitnessBrowser__Pedo557:CA265_RS17585 331 LNPDVINVNGGAIALGHPLGCTGAKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFE 389 88******************************************************997 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 7.27 // [ok]
This GapMind analysis is from Sep 17 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