Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf6N2E2_2113 Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 Length = 393 Score = 715 bits (1846), Expect = 0.0 Identities = 365/393 (92%), Positives = 379/393 (96%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 MQ+VVIVAATRTA+GSFQGSLASIPAPELGAAVIR LLEQTGL QVDEVILGQVLTAG Sbjct: 1 MQEVVIVAATRTAIGSFQGSLASIPAPELGAAVIRHLLEQTGLSGEQVDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 SGQNPARQASILAGLPHAVP+LTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL Sbjct: 61 SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISRE QDAFAA Sbjct: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 ASQQKA AAIE GRF DEITPILIPQRKGDPVAFA DEQPRAGTTAESL KLKPAFKKDG Sbjct: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASSLNDGAAAV+LMSA+KAKALGLPVLA+I++YANAGVDPAIMGIGPVSATRRC Sbjct: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 LDKAGWSL LDLIEANEAFAAQSLAV +EL+WD +KVNVNGGAIA+GHPIGASGCRVLV Sbjct: 301 LDKAGWSLDQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393 +LLHEMIKRDAKKGLATLCIGGGQGVALALER+ Sbjct: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALERA 393 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: 604 Number of extensions: 14 Number of successful extensions: 1 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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 Pf6N2E2_2113 (Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.4468.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-153 496.0 5.5 3.9e-153 495.9 5.5 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 Acetyl-CoA acetyltransferase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 Acetyl-CoA acetyltransferase (EC 2.3.1.9) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.9 5.5 3.9e-153 3.9e-153 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 495.9 bits; conditional E-value: 3.9e-153 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaRea 64 iv+a+Rt+ig+++gsl++++a +L+aavi++lle++gl+ e++devilG+vl+ag+++n+aR+a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 6 IVAATRTAIGSFQGSLASIPAPELGAAVIRHLLEQTGLSGEQVDEVILGQVLTAGSGQNPARQA 69 8*************************************************************** PP TIGR01930 65 alaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrres 128 + aglp+ vpalt+n+vC+Sgl+A++l+aq+i++G+a+v++aGG+E+mS +p++l+a+ r + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 70 SILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYVLPAA--RTG 131 *********************************************************98..89* PP TIGR01930 129 lklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkf 189 l++g+ak+ d+++ d+ + ++++mg+tAenl +kygisReeqD++a++S+qka +Aie g+f lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 132 LRMGHAKMIDSMITDGlwdAFNDYHMGITAENLVDKYGISREEQDAFAAASQQKAVAAIEGGRF 195 *******************99******************************************* PP TIGR01930 190 kdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaal 250 +dei+p+ ++++ ++ +++De++r++tt+e+L+kLkpafk+ +gs vtAgN+s+lnDGAaa+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 196 ADEITPILIPQRkgdPVAFATDEQPRAGTTAESLGKLKPAFKK-DGS-VTAGNASSLNDGAAAV 257 *********9999999*************************95.9*7.**************** PP TIGR01930 251 llmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFA 314 +lms e+ak+lgl +la+i ++a+agvdp++mg+gpv A++++L+kag+s++++dl+E nEAFA lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 258 ILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRCLDKAGWSLDQLDLIEANEAFA 321 **************************************************************** PP TIGR01930 315 aqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGq 378 aq lav++el+ d +kvNvnGGAiAlGHP+GasG+r++++ll+e+ +r++k GlatlC+ggGq lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 322 AQSLAVARELK-WDMDKVNVNGGAIALGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQ 384 ***********.88************************************************** PP TIGR01930 379 GaAvile 385 G+A+ le lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2113 385 GVALALE 391 ***9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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: 9.63 // [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