Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_066920982.1 ACG33_RS10385 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_001579945.1:WP_066920982.1 Length = 370 Score = 505 bits (1301), Expect = e-148 Identities = 240/357 (67%), Positives = 296/357 (82%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G+LF V++FGESHG A+GCIVDG PPG+PL+E D+Q +++RRR GTSR+T+QR+ Sbjct: 1 MSGNTFGKLFCVSSFGESHGPAMGCIVDGCPPGLPLSEQDIQPEIERRRTGTSRHTSQRK 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPDQV+ILSGVFEG TTGT IGLLIEN DQRS+DY +KD FRPGHADYTY+QKYG RDY Sbjct: 61 EPDQVRILSGVFEGRTTGTPIGLLIENQDQRSRDYDKVKDRFRPGHADYTYQQKYGRRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARET MRVAAGAIA+KYL E+ G+ I+G L Q+G + L+++ V NPFF Sbjct: 121 RGGGRSSARETVMRVAAGAIARKYLRERLGVTIQGYLAQLGPLRLEVRSLRTVYDNPFFS 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDP ++ +++ M L+++GDS+GA++ V+A GVP GLGEP+FDRLDADIAHA+MSINAV Sbjct: 181 PDPSRLTEIEDYMTQLRRDGDSVGARINVLARGVPPGLGEPIFDRLDADIAHAMMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVE+G GF+ VA RGS++RD ++ GF SNHAGG+LGGISSGQ I+ +A KPTSSI + Sbjct: 241 KGVELGAGFESVAQRGSEHRDLMSPQGFLSNHAGGVLGGISSGQDILVSLAFKPTSSIVI 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTD 357 PG TI+ G VE++T GRHDPCVG+RA PIAEAMLA+VLMDH LR RAQNADV D Sbjct: 301 PGETIDIQGRSVEVVTTGRHDPCVGLRATPIAEAMLALVLMDHYLRHRAQNADVAPD 357 Lambda K H 0.319 0.138 0.404 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: 473 Number of extensions: 8 Number of successful extensions: 2 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: 361 Length of database: 370 Length adjustment: 30 Effective length of query: 331 Effective length of database: 340 Effective search space: 112540 Effective search space used: 112540 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_066920982.1 ACG33_RS10385 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))
# 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.aa/TIGR00033.hmm # target sequence database: /tmp/gapView.3981.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00033 [M=351] Accession: TIGR00033 Description: aroC: chorismate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-141 455.9 0.0 4.6e-141 455.7 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066920982.1 ACG33_RS10385 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066920982.1 ACG33_RS10385 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.7 0.0 4.6e-141 4.6e-141 3 350 .. 12 350 .. 10 351 .. 0.97 Alignments for each domain: == domain 1 score: 455.7 bits; conditional E-value: 4.6e-141 TIGR00033 3 lttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaP 71 + fGeSHg+a+g+i+dG+P+gl+l+e+diq+e++rRr g+sr+t++rkE D+v+ilsGvfeG+TtG+P lcl|NCBI__GCF_001579945.1:WP_066920982.1 12 VSSFGESHGPAMGCIVDGCPPGLPLSEQDIQPEIERRRTGTSRHTSQRKEPDQVRILSGVFEGRTTGTP 80 678****************************************************************** PP TIGR00033 72 iallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140 i lli+N+d+rs+dy+++k+++RPgHadyty++KYg +d++gggrsSaReT++rvaaGa+a+k+L+e lcl|NCBI__GCF_001579945.1:WP_066920982.1 81 IGLLIENQDQRSRDYDKVKDRFRPGHADYTYQQKYGRRDYRGGGRSSARETVMRVAAGAIARKYLRERL 149 ********************************************************************* PP TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsn 209 g+ i +y+ +lg ++le +s +++ ++p++ pd+++ e+e++++++++dgdsvG++++v++++ lcl|NCBI__GCF_001579945.1:WP_066920982.1 150 GVTIQGYLAQLGPLRLEVRSL-----RTVYDNPFFSPDPSRLTEIEDYMTQLRRDGDSVGARINVLARG 213 *************99996444.....45777************************************** PP TIGR00033 210 vpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieG 278 vp glGep+fd+lda +a+a++sinAvKgve+G+GFe++ +rGse+ D + + + +n+ GG++G lcl|NCBI__GCF_001579945.1:WP_066920982.1 214 VPPGLGEPIFDRLDADIAHAMMSINAVKGVELGAGFESVAQRGSEHRDLM----SPQGFLSNHAGGVLG 278 ************************************************44....45679********** PP TIGR00033 279 GitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallek 347 Gi+ G+di v+ a+Kp+++i p +t+d++++ +t+gRhDpcv +ra+p++Eam+alvl+d++l++ lcl|NCBI__GCF_001579945.1:WP_066920982.1 279 GISSGQDILVSLAFKPTSSIVIPGETIDIQGRSVEVVTTGRHDPCVGLRATPIAEAMLALVLMDHYLRH 347 ********************************************************************* PP TIGR00033 348 ras 350 ra+ lcl|NCBI__GCF_001579945.1:WP_066920982.1 348 RAQ 350 987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (370 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: 9.50 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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