Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate GFF2751 HP15_2695 acetyl-CoA acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Marino:GFF2751 Length = 415 Score = 811 bits (2094), Expect = 0.0 Identities = 415/415 (100%), Positives = 415/415 (100%) Query: 1 MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY 60 MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY Sbjct: 1 MSADNILKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLY 60 Query: 61 GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA 120 GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA Sbjct: 61 GCANQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIA 120 Query: 121 GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF 180 GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF Sbjct: 121 GGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADF 180 Query: 181 GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL 240 GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL Sbjct: 181 GISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKL 240 Query: 241 ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM 300 ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM Sbjct: 241 ASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIM 300 Query: 301 GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL 360 GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL Sbjct: 301 GFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIAL 360 Query: 361 GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA 415 GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA Sbjct: 361 GHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMDAVA 415 Lambda K H 0.318 0.133 0.382 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: 726 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: 415 Length of database: 415 Length adjustment: 31 Effective length of query: 384 Effective length of database: 384 Effective search space: 147456 Effective search space used: 147456 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 GFF2751 HP15_2695 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))
# 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/TIGR02430.hmm # target sequence database: /tmp/gapView.32375.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02430 [M=400] Accession: TIGR02430 Description: pcaF: 3-oxoadipyl-CoA thiolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-223 727.7 6.0 2.1e-223 727.5 6.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2751 HP15_2695 acetyl-CoA acetyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2751 HP15_2695 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 727.5 6.0 2.1e-223 2.1e-223 1 400 [] 8 411 .. 8 411 .. 0.98 Alignments for each domain: == domain 1 score: 727.5 bits; conditional E-value: 2.1e-223 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaG 75 k++yivdairtpiGrygG+ls+vraddl+a+p+kal +r+p+ld+++iddv++GcanqaGednr+varm++llaG lcl|FitnessBrowser__Marino:GFF2751 8 KDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGEDNRDVARMSLLLAG 82 689************************************************************************ PP TIGR02430 76 lpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvn 150 lpv+vpg+t+nrlcgsg+da+g aarai++Ge++l+iaGGvesmsrapfv+Gkadsafsr+a+++dttiGwrfvn lcl|FitnessBrowser__Marino:GFF2751 83 LPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVN 157 *************************************************************************** PP TIGR02430 151 pklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehl 225 p lk++yG+dsmpetaenva +fg+sredqdafalrsqqrtaaaq++G +a+ei+pv+i+++k ++ vvd+deh+ lcl|FitnessBrowser__Marino:GFF2751 158 PVLKKQYGIDSMPETAENVAADFGISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHP 232 *************************************************************************** PP TIGR02430 226 raettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvp 300 r et+le+la l +++re+gtvtaGnasGvndGa+allla+++a+k+++l+prar++a+a+aGvepr+mG+gp+p lcl|FitnessBrowser__Marino:GFF2751 233 R-ETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGPAP 306 *.************************************************************************* PP TIGR02430 301 avkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqlek 375 a++k+la agl+l+d+dvielneafaaqalav+r+lgl+dd+++vnpnGGaialGhplG+sGarlv+tal++le+ lcl|FitnessBrowser__Marino:GFF2751 307 ATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPLGMSGARLVTTALNELER 381 *************************************************************************98 PP TIGR02430 376 s.....ggryalatlciGvGqGialvierv 400 + + ryal+t+ciGvGqGial+ier+ lcl|FitnessBrowser__Marino:GFF2751 382 RhaagqKARYALCTMCIGVGQGIALIIERM 411 633222469*******************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (415 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: 00:00:00.02 # Mc/sec: 7.80 // [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