Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982 (397 letters) >FitnessBrowser__PS:Dsui_0976 Length = 393 Score = 520 bits (1339), Expect = e-152 Identities = 261/390 (66%), Positives = 319/390 (81%) Query: 5 NDPIVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAG 64 +DPIVIVS RTPMGGFQG+ SLTAPQLGA AIKAAVERAG+ + V+EV+FG VL AG Sbjct: 2 SDPIVIVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAG 61 Query: 65 LGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSN 124 +GQAPARQAALGAGL S CTT++K+CGS +++ ++ HD LLAGS ++ VAGG ESMSN Sbjct: 62 VGQAPARQAALGAGLPLSAGCTTIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSN 121 Query: 125 APYLLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAFA 184 APYLL +AR GYR+GHG++ D MF DGLEDAY KGRLMGTFAE+CAE+ GF+REAQD +A Sbjct: 122 APYLLPKARGGYRLGHGQLLDHMFFDGLEDAYQKGRLMGTFAEECAESYGFTREAQDEWA 181 Query: 185 IASTTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGGT 244 I ST RAQ+AIK+G FK EI P+T+ K VV+ DEQP KA+++KI +LKPAF++ GT Sbjct: 182 IQSTVRAQKAIKEGLFKWEIAPVTIAGKKGDVVVDQDEQPLKAQIEKIPALKPAFKKDGT 241 Query: 245 VTAANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKLM 304 VTAANSSSISDGAAALVLM++S+A+ GL P+A I GH A P LF AP+ A++KLM Sbjct: 242 VTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTAPVFAMEKLM 301 Query: 305 KKTGWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILVT 364 +KTGW++ DVDL E+NEAFAVV MAA+ L++ K+NVHGGACALGHPIGASGARILVT Sbjct: 302 QKTGWNVADVDLWEINEAFAVVTMAAIKDLKLDPAKVNVHGGACALGHPIGASGARILVT 361 Query: 365 LLSALRQKGLKRGVAAICIGGGEATAMAVE 394 L+ AL+Q G K+GVA++CIGGGEA A+ VE Sbjct: 362 LIGALKQYGKKKGVASLCIGGGEAVAVGVE 391 Lambda K H 0.318 0.132 0.376 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: 548 Number of extensions: 15 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: 397 Length of database: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 Dsui_0976 Dsui_0976 (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.17165.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-134 432.9 3.4 6.1e-134 432.7 3.4 1.0 1 lcl|FitnessBrowser__PS:Dsui_0976 Dsui_0976 acetyl-CoA acetyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0976 Dsui_0976 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.7 3.4 6.1e-134 6.1e-134 1 384 [. 7 390 .. 7 391 .. 0.98 Alignments for each domain: == domain 1 score: 432.7 bits; conditional E-value: 6.1e-134 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpal 77 iv+ +Rtp+g ++g +++l+a +L+a++ik+++erag++pe+++ev++Gnvlqag ++++aR+aal aglp s + lcl|FitnessBrowser__PS:Dsui_0976 7 IVSVARTPMGGFQGDFNSLTAPQLGATAIKAAVERAGIKPEQVEEVVFGNVLQAGVGQAPARQAALGAGLPLSAGCT 83 89********99***************************************************************** PP TIGR01930 78 tvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl....vktkls 150 t+++vC+S+l++v+++ +++ aG +++ vaGG EsmS++p+ll+++ r +++lg+ +l d++ d+ +++ lcl|FitnessBrowser__PS:Dsui_0976 84 TIHKVCGSALKSVMMVHDSLLAGSYEIGVAGGQESMSNAPYLLPKA--RGGYRLGHGQLLDHMFFDGledaYQKGRL 158 ********************************************98..89***********999998999988999* PP TIGR01930 151 mgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkp 225 mg+ Ae++a+ yg++Re qDe+a++S +a+kAi+eg fk ei pv++ gk ++vv++De++ + ++ek+ Lkp lcl|FitnessBrowser__PS:Dsui_0976 159 MGTFAEECAESYGFTREAQDEWAIQSTVRAQKAIKEGLFKWEIAPVTIAGKkgDVVVDQDEQPL-KAQIEKIPALKP 234 **************************************************99888888888887.89********** PP TIGR01930 226 afkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsis 302 afk+ +g tvtA+Nss+++DGAaal+lm+e++ak lgl p+a+iv++++ + +p+ ++++pv A+ek+++k+g+++ lcl|FitnessBrowser__PS:Dsui_0976 235 AFKK-DG-TVTAANSSSISDGAAALVLMKESKAKVLGLAPIAKIVGHTTHAQEPNLFTTAPVFAMEKLMQKTGWNVA 309 **95.9*.6******************************************************************** PP TIGR01930 303 didlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqG 379 d+dl+EinEAFA++++a++k+l+ ld++kvNv+GGA AlGHP+GasGari++tl+ +Lk+ gkk G+a+lC+ggG + lcl|FitnessBrowser__PS:Dsui_0976 310 DVDLWEINEAFAVVTMAAIKDLK-LDPAKVNVHGGACALGHPIGASGARILVTLIGALKQYGKKKGVASLCIGGGEA 385 ***********************.99*************************************************** PP TIGR01930 380 aAvil 384 +Av + lcl|FitnessBrowser__PS:Dsui_0976 386 VAVGV 390 **966 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.24 // [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