Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate SMc02228 SMc02228 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >FitnessBrowser__Smeli:SMc02228 Length = 402 Score = 250 bits (639), Expect = 4e-71 Identities = 150/411 (36%), Positives = 221/411 (53%), Gaps = 33/411 (8%) Query: 1 MKEAVIVSGARTPVGKAKK-GSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATP 59 M + + RTP G+ KK G+L V L A ++ R G +DD+I+GC P Sbjct: 1 MTKVFVYDHVRTPRGRGKKDGALHEVPSVRLAAKVLEAVRDRNGLDTSTVDDVIMGCVDP 60 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 + G + + AG P + ++R+C+SGL ++ + A KI GA D IAGG ES Sbjct: 61 VMDAGAVIPKAAAFEAGYSTRAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVES 120 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 MS+V + + + P Y+M G +A+ +A KYG SR+D DA+AV S + AA A Sbjct: 121 MSRVGLGMSGGAWFMDPSVNLPAYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAANA 180 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239 +G FK+ +VPV K + +DE +RP T L++L P+F + G Sbjct: 181 WEKGYFKNSVVPV-----------KDQNGLVILDRDEHMRPGTDMQALASLNPSFQMPGE 229 Query: 240 VT---------------------AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFA 278 + AGNSS DGAAAV++ + +A+GL P + R+FA Sbjct: 230 MGGFEAVGIQAHPEIERINYVHHAGNSSGIVDGAAAVLIGSKAGGEAMGLKPRARIRAFA 289 Query: 279 VGGVPPEVMGIGPVEAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNV 338 G P +M GPV+ + LK A ++L DI LFELNEAFA+ ++ + I +K+NV Sbjct: 290 NIGSDPALMLTGPVDVTEKLLKRADMKLSDIDLFELNEAFAAVVLRYCQAFDIPHDKINV 349 Query: 339 NGGAIALGHPLGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 NGGAIA+GHPLG TG + +++ E++RR+ +VT+CIG GMG A + E Sbjct: 350 NGGAIAMGHPLGATGAMILGTVLDELERRDLNTALVTLCIGAGMGTATIIE 400 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: 438 Number of extensions: 21 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: 402 Length adjustment: 31 Effective length of query: 360 Effective length of database: 371 Effective search space: 133560 Effective search space used: 133560 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 SMc02228 SMc02228 (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.6385.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-126 408.4 0.3 1.7e-126 408.2 0.3 1.0 1 lcl|FitnessBrowser__Smeli:SMc02228 SMc02228 acetyl-CoA acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02228 SMc02228 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.2 0.3 1.7e-126 1.7e-126 1 385 [] 6 400 .. 6 400 .. 0.95 Alignments for each domain: == domain 1 score: 408.2 bits; conditional E-value: 1.7e-126 TIGR01930 1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 ++d vRtp g k g+l+e++++ L+a+v++++ +r+gld + +d+vi+G+v + + a i + aa++ag ++ lcl|FitnessBrowser__Smeli:SMc02228 6 VYDHVRTPRGrgKKDGALHEVPSVRLAAKVLEAVRDRNGLDTSTVDDVIMGCVDPVMDAgAVIPKAAAFEAGYST 80 6799*******988********************************************99*************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdlvkt 147 + p+++++r+CaSgl+Av+ +a+ki+ G+ d+v+aGGvEsmSrv ++++ ++ +++ +l + lcl|FitnessBrowser__Smeli:SMc02228 81 RAPGMQISRFCASGLDAVNFGAAKIAQGADDIVIAGGVESMSRVGLGMSGG--AWFMDPSV-NL--------PAY 144 ********************************************9999987..88999822.22........356 PP TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpnttlekLak 222 +++g++A+ +a+kyg+sR+++D+ya++S+++aa+A+e+g+fk+++vpv+ ++ +++++De++rp+t +++La+ lcl|FitnessBrowser__Smeli:SMc02228 145 FMPQGVSADLIATKYGFSRDDVDAYAVESQKRAANAWEKGYFKNSVVPVKDQNGLVILDRDEHMRPGTDMQALAS 219 89************************************************99889******************** PP TIGR01930 223 Lkpafkekkgs....................tvtAgNssqlnDGAaalllmseevakelgltplarivsaavagv 277 L+p f+ g+ +++AgNss++ DGAaa+l+ s++ +++gl+p ari+++a++g+ lcl|FitnessBrowser__Smeli:SMc02228 220 LNPSFQM-PGEmggfeavgiqahpeierinyVHHAGNSSGIVDGAAAVLIGSKAGGEAMGLKPRARIRAFANIGS 293 *****98.344455667777777888888889******************************************* PP TIGR01930 278 dpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGari 352 dp+ m++gpv +ek+Lk+a++++sdidl+E+nEAFAa+vl ++++ + ++k+NvnGGAiA+GHPlGa+Ga+i lcl|FitnessBrowser__Smeli:SMc02228 294 DPALMLTGPVDVTEKLLKRADMKLSDIDLFELNEAFAAVVLRYCQAFD-IPHDKINVNGGAIAMGHPLGATGAMI 367 ************************************************.88************************ PP TIGR01930 353 vltllkeLkergkkyGlatlCvggGqGaAvile 385 + t+l+eL++r+ + +l+tlC+g G+G+A+i+e lcl|FitnessBrowser__Smeli:SMc02228 368 LGTVLDELERRDLNTALVTLCIGAGMGTATIIE 400 *******************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (402 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: 10.41 // [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