Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 Length = 393 Score = 674 bits (1739), Expect = 0.0 Identities = 337/393 (85%), Positives = 371/393 (94%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 MQ+VVIVAATRTA+GSFQGSLA++ A +LGAAVIR+LL QTGLDPAQVDEVI+GQVLTAG Sbjct: 1 MQEVVIVAATRTAIGSFQGSLANVSAVDLGAAVIRQLLAQTGLDPAQVDEVIMGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQA+I AGLP AVP++TLNKVCGSGLKALHL AQAIRCGDAEVIIAGG ENMSL Sbjct: 61 AGQNPARQAAIKAGLPFAVPAMTLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 + YV+P ARTGLRMGHA+++D+MI+DGLWDAFNDYHMGITAENL +KY ++RE QDAFAA Sbjct: 121 SNYVMPGARTGLRMGHAQIVDTMISDGLWDAFNDYHMGITAENLAEKYSLTREQQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 ASQQKA AAIEAGRF DEITPILIPQRKGDP++FA DEQPRAGTTA+SL KLK AFKKDG Sbjct: 181 ASQQKAVAAIEAGRFADEITPILIPQRKGDPLSFATDEQPRAGTTADSLGKLKAAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASSLNDGAAAV+LMSA+KAKALGLPVLA+IA+YANAGVDPAIMGIGPVSATRRC Sbjct: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKIAAYANAGVDPAIMGIGPVSATRRC 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 LDK GWS+G LDLIEANEAFAAQSLAV K+LEWD KVNVNGGAIA+GHPIGASGCRVLV Sbjct: 301 LDKTGWSIGQLDLIEANEAFAAQSLAVAKDLEWDLNKVNVNGGAIALGHPIGASGCRVLV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393 TLLHEMIK+DAKKGLATLCIGGGQGVALA+ER+ Sbjct: 361 TLLHEMIKQDAKKGLATLCIGGGQGVALAIERA 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: 559 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 Pf1N1B4_5835 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ 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.31592.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-151 490.3 11.3 2.2e-151 490.1 11.3 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 490.1 11.3 2.2e-151 2.2e-151 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 490.1 bits; conditional E-value: 2.2e-151 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaRea 64 iv+a+Rt+ig+++gsl+++sa+dL+aavi++ll+++gldp+++devi+G+vl+ag+++n+aR+a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 6 IVAATRTAIGSFQGSLANVSAVDLGAAVIRQLLAQTGLDPAQVDEVIMGQVLTAGAGQNPARQA 69 8*************************************************************** PP TIGR01930 65 alaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrres 128 a++aglp vpa+t+n+vC+Sgl+A++laaq+i++G+a+v++aGG E+mS + ++++ + r + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 70 AIKAGLPFAVPAMTLNKVCGSGLKALHLAAQAIRCGDAEVIIAGGQENMSLSNYVMPGA--RTG 131 *******************************************************9997..89* PP TIGR01930 129 lklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkf 189 l++g+a+ d++++d+ + ++++mg+tAenla+ky+++Re+qD++a++S+qka +Aie+g+f lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 132 LRMGHAQIVDTMISDGlwdAFNDYHMGITAENLAEKYSLTREQQDAFAAASQQKAVAAIEAGRF 195 *******************99******************************************* PP TIGR01930 190 kdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaal 250 +dei+p+ ++++ + ++++De++r++tt+++L+kLk+afk+ +gs vtAgN+s+lnDGAaa+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 196 ADEITPILIPQRkgdPLSFATDEQPRAGTTADSLGKLKAAFKK-DGS-VTAGNASSLNDGAAAV 257 *********99999999************************95.9*7.**************** PP TIGR01930 251 llmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFA 314 +lms e+ak+lgl +la+i ++a+agvdp++mg+gpv A++++L+k+g+si ++dl+E nEAFA lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 258 ILMSAEKAKALGLPVLAKIAAYANAGVDPAIMGIGPVSATRRCLDKTGWSIGQLDLIEANEAFA 321 **************************************************************** PP TIGR01930 315 aqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGq 378 aq lav+k+l+ dl+kvNvnGGAiAlGHP+GasG+r+++tll+e+ ++++k GlatlC+ggGq lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 322 AQSLAVAKDLE-WDLNKVNVNGGAIALGHPIGASGCRVLVTLLHEMIKQDAKKGLATLCIGGGQ 384 ***********.88************************************************** PP TIGR01930 379 GaAvile 385 G+A+ +e lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5835 385 GVALAIE 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.19 // [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