Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >lcl|FitnessBrowser__Putida:PP_4636 PP_4636 acetyl-CoA acetyltransferase Length = 392 Score = 660 bits (1704), Expect = 0.0 Identities = 332/392 (84%), Positives = 366/392 (93%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 M DVVIVAATRTA+GSFQG+LA++PA +LGAAVI++LL+QTGLDPAQVDEVILGQVLTAG Sbjct: 1 MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQA+I AGLP +VP+LTLNKVCGSGLKALHL AQAIRCGDAEV+IAGG ENMSL Sbjct: 61 AGQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYV+P+ARTG RMGH ++IDSMITDGLWDAFNDYHMGITAENLVDKYG+SRE QDAFAA Sbjct: 121 APYVMPSARTGQRMGHGQLIDSMITDGLWDAFNDYHMGITAENLVDKYGLSREQQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 SQ+KA AAIEAGRF EITPI++PQ+KG+P FA DEQPR TTAESLAKL+PAFKKDG Sbjct: 181 ESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKLRPAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNASSLNDGAAAVLLMSA KA+ALGLPVLA+IA+YA+AGVDPAIMGIGPVSAT+RC Sbjct: 241 SVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRC 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 LDKAGW L +LDLIEANEAFAAQ+LAVG L WDA +VNVNGGAIA+GHPIGASGCRVLV Sbjct: 301 LDKAGWQLAELDLIEANEAFAAQALAVGNALAWDAARVNVNGGAIALGHPIGASGCRVLV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 TLLHEMIKRD KKGLATLCIGGGQGVALA+ER Sbjct: 361 TLLHEMIKRDVKKGLATLCIGGGQGVALAIER 392 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: 556 Number of extensions: 12 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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 PP_4636 PP_4636 (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.9812.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-152 492.1 8.1 6.3e-152 491.9 8.1 1.0 1 lcl|FitnessBrowser__Putida:PP_4636 PP_4636 acetyl-CoA acetyltransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4636 PP_4636 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 491.9 8.1 6.3e-152 6.3e-152 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 491.9 bits; conditional E-value: 6.3e-152 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvp 75 iv+a+Rt+ig+++g+l++++a+dL+aavik+ll+++gldp+++devilG+vl+ag+++n+aR+aa++aglp svp lcl|FitnessBrowser__Putida:PP_4636 6 IVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAGAGQNPARQAAIKAGLPFSVP 80 8************************************************************************** PP TIGR01930 76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147 alt+n+vC+Sgl+A++laaq+i++G+a+vv+aGG E+mS +p++++++ r + ++g+ +l d+++ d+ + + lcl|FitnessBrowser__Putida:PP_4636 81 ALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSLAPYVMPSA--RTGQRMGHGQLIDSMITDGlwdAFN 153 **********************************************97..89999*****************99* PP TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlek 219 +++mg+tAenl +kyg+sRe+qD++a++S++ka +Aie+g+f++ei+p+++++k +kv+++De++rp+tt+e+ lcl|FitnessBrowser__Putida:PP_4636 154 DYHMGITAENLVDKYGLSREQQDAFAAESQRKAVAAIEAGRFDAEITPIVLPQKkgePKVFARDEQPRPDTTAES 228 ***************************************************9999******************** PP TIGR01930 220 LakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaL 294 LakL+pafk+ +gs vtAgN+s+lnDGAaa+llms ++a++lgl +la+i ++a agvdp++mg+gpv A++++L lcl|FitnessBrowser__Putida:PP_4636 229 LAKLRPAFKK-DGS-VTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRCL 301 ********95.9*7.************************************************************ PP TIGR01930 295 kkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGl 369 +kag+++ ++dl+E nEAFAaq+lav ++l+ d ++vNvnGGAiAlGHP+GasG+r+++tll+e+ +r++k Gl lcl|FitnessBrowser__Putida:PP_4636 302 DKAGWQLAELDLIEANEAFAAQALAVGNALA-WDAARVNVNGGAIALGHPIGASGCRVLVTLLHEMIKRDVKKGL 375 *******************************.88***************************************** PP TIGR01930 370 atlCvggGqGaAvile 385 atlC+ggGqG+A+ +e lcl|FitnessBrowser__Putida:PP_4636 376 ATLCIGGGQGVALAIE 391 ************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 7.65 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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