Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__Koxy:BWI76_RS23445 Length = 391 Score = 533 bits (1374), Expect = e-156 Identities = 260/392 (66%), Positives = 328/392 (83%), Gaps = 1/392 (0%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 M+DVVIV A RT +G FQG+L+ A ELG+ V++ L+E++G+DP +DEVILGQVLTAG Sbjct: 1 MKDVVIVGALRTPIGCFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQ++I GLP+ V ++T+N VCGSGLKALHL QAI+CG+A+V+IAGG ENMS Sbjct: 61 TGQNPARQSAIRGGLPNTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENMSR 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 AP+VL +RTG ++G++++IDS++ DGLWDAFNDYHMG+TAENL +YGISRE QDA+A Sbjct: 121 APHVLTDSRTGAQLGNSQLIDSLVHDGLWDAFNDYHMGVTAENLAREYGISRELQDAWAL 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 +SQ KA AI++GRF DEI P+ + G P DEQPR +AE+LA L P F + G Sbjct: 181 SSQHKARRAIDSGRFRDEIVPVT-SELNGIPRLVDTDEQPRVDPSAEALASLLPTFDQQG 239 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASS+NDGAAAV++MS KA+ALGLP+LARI ++A+ GVDPA+MGI PV ATRRC Sbjct: 240 SVTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDPALMGIAPVHATRRC 299 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 L++AGW L ++DLIEANEAFAAQ+++VG+ LEWD +VNVNGGAIA+GHPIGASGCR+LV Sbjct: 300 LERAGWKLDEVDLIEANEAFAAQAISVGRVLEWDERRVNVNGGAIALGHPIGASGCRILV 359 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 +L+HEMIKRDA+KGLATLCIGGGQGVALA+ER Sbjct: 360 SLVHEMIKRDARKGLATLCIGGGQGVALAVER 391 Lambda K H 0.317 0.133 0.378 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: 471 Number of extensions: 16 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate BWI76_RS23445 BWI76_RS23445 (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.1952624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-147 477.0 1.4 2.3e-147 476.9 1.4 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS23445 BWI76_RS23445 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 476.9 1.4 2.3e-147 2.3e-147 1 385 [] 6 390 .. 6 390 .. 0.99 Alignments for each domain: == domain 1 score: 476.9 bits; conditional E-value: 2.3e-147 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglp 71 iv+a+Rtpig ++g+l+ sa++L++ v+k+l+er+g+dp+ idevilG+vl+ag+++n+aR+ a++ glp lcl|FitnessBrowser__Koxy:BWI76_RS23445 6 IVGALRTPIGCFQGTLSRHSAVELGSVVVKALVERSGVDPQSIDEVILGQVLTAGTGQNPARQSAIRGGLP 76 89********99*********************************************************** PP TIGR01930 72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllk 142 ++v+a+t+n vC+Sgl+A++la q+i++Geadvv+aGG E+mSr+p++l +s r +++lg+++l d+l++ lcl|FitnessBrowser__Koxy:BWI76_RS23445 77 NTVSAITINDVCGSGLKALHLATQAIQCGEADVVIAGGQENMSRAPHVLTDS--RTGAQLGNSQLIDSLVH 145 **************************************************98..89*************** PP TIGR01930 143 dl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskD 208 d+ + ++++mg+tAenla++ygisRe qD++al+S++ka +Ai++g+f deivpv+ + + ++ v++D lcl|FitnessBrowser__Koxy:BWI76_RS23445 146 DGlwdAFNDYHMGVTAENLAREYGISRELQDAWALSSQHKARRAIDSGRFRDEIVPVTSELNgiPRLVDTD 216 *****99****************************************************999********* PP TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdp 279 e++r + ++e+La+L p f++ +gs vtAgN+s++nDGAaa+++mse++a++lgl +lari+++a +gvdp lcl|FitnessBrowser__Koxy:BWI76_RS23445 217 EQPRVDPSAEALASLLPTFDQ-QGS-VTAGNASSINDGAAAVMMMSETKAEALGLPILARIRAFASVGVDP 285 *******************95.8*7.********************************************* PP TIGR01930 280 eemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGa 350 + mg++pv+A++++L++ag++++++dl+E nEAFAaq++ v + l+ d+ +vNvnGGAiAlGHP+GasG+ lcl|FitnessBrowser__Koxy:BWI76_RS23445 286 ALMGIAPVHATRRCLERAGWKLDEVDLIEANEAFAAQAISVGRVLE-WDERRVNVNGGAIALGHPIGASGC 355 **********************************************.88********************** PP TIGR01930 351 rivltllkeLkergkkyGlatlCvggGqGaAvile 385 ri+++l++e+ +r+++ GlatlC+ggGqG+A+ +e lcl|FitnessBrowser__Koxy:BWI76_RS23445 356 RILVSLVHEMIKRDARKGLATLCIGGGQGVALAVE 390 *******************************9886 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.33 // [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