Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_074201084.1 BUQ81_RS03880 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_900141795.1:WP_074201084.1 Length = 365 Score = 523 bits (1348), Expect = e-153 Identities = 261/360 (72%), Positives = 306/360 (85%), Gaps = 1/360 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGNT+G+LFRVTT GESHG AL CIVDG PPG+ L+EAD+Q DLDRRRPG+S++TT RR Sbjct: 1 MAGNTLGELFRVTTAGESHGPALVCIVDGCPPGMELSEADIQPDLDRRRPGSSKFTTPRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D VKILSGVFEG TTGT I ++IENTDQRS+DY +I FRP HADYTY QKYG+RDY Sbjct: 61 EADHVKILSGVFEGKTTGTPIAMVIENTDQRSKDYGSIAQTFRPAHADYTYLQKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYL E+ G+EI G ++Q+G + ++ + S ++ NP FC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLRERIGVEIFGYVSQIGPVAIEKVERSFIDTNPLFC 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDP+ + +++ + LKK GDSIGAKV+VVASGVP GLGEPVFDRLDADIA +LMSINAV Sbjct: 181 PDPEALPKMEQFLIDLKKTGDSIGAKVSVVASGVPVGLGEPVFDRLDADIAKSLMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEIT-KDGFQSNHAGGILGGISSGQQIIAHMALKPTSSIT 299 KGVEIGDGF VV RGS++RDEIT ++GF SNHAGG++GGIS+GQ I+AH+ALKPTSSIT Sbjct: 241 KGVEIGDGFAVVNQRGSEHRDEITPEEGFLSNHAGGVVGGISTGQDIVAHIALKPTSSIT 300 Query: 300 VPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 VPGR++ R E VEMITKGRHDPCVGIRAVPIAEA LAIVLMDH LR RAQNADV+ +P Sbjct: 301 VPGRSVTRNMEAVEMITKGRHDPCVGIRAVPIAEAQLAIVLMDHYLRHRAQNADVEPPMP 360 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: 463 Number of extensions: 9 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: 365 Length adjustment: 29 Effective length of query: 332 Effective length of database: 336 Effective search space: 111552 Effective search space used: 111552 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_074201084.1 BUQ81_RS03880 (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.11728.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-147 476.4 0.4 2.8e-147 476.2 0.4 1.0 1 lcl|NCBI__GCF_900141795.1:WP_074201084.1 BUQ81_RS03880 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900141795.1:WP_074201084.1 BUQ81_RS03880 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 476.2 0.4 2.8e-147 2.8e-147 1 350 [. 10 351 .. 10 352 .. 0.98 Alignments for each domain: == domain 1 score: 476.2 bits; conditional E-value: 2.8e-147 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHg+al++i+dG+P+g+el+e+diq++l+rRrpg+s++t++r+E+D+v+ilsGvfeGkTtG lcl|NCBI__GCF_900141795.1:WP_074201084.1 10 FRVTTAGESHGPALVCIVDGCPPGMELSEADIQPDLDRRRPGSSKFTTPRREADHVKILSGVFEGKTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pia++i+N+d+rskdy +i++++RP+Hadytyl+KYgi+d++gggrsSaReTa+rvaaGa+akk+L+e lcl|NCBI__GCF_900141795.1:WP_074201084.1 79 TPIAMVIENTDQRSKDYGSIAQTFRPAHADYTYLQKYGIRDYRGGGRSSARETAMRVAAGAIAKKYLRE 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 g+ei +yv+++g v++e+ + + +d++p++cpd+ea +me+ + +kk gds+G++v+vv+ lcl|NCBI__GCF_900141795.1:WP_074201084.1 148 RIGVEIFGYVSQIGPVAIEK-----VERSFIDTNPLFCPDPEALPKMEQFLIDLKKTGDSIGAKVSVVA 211 ******************96.....446779************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 s+vpvglGep+fd+lda +a+ l+sinAvKgveiGdGF+ +++rGse+ De++ e++ + +n+ GG+ lcl|NCBI__GCF_900141795.1:WP_074201084.1 212 SGVPVGLGEPVFDRLDADIAKSLMSINAVKGVEIGDGFAVVNQRGSEHRDEITPEEG---FLSNHAGGV 277 ***************************************************998875...89******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 GGi++G+di+ +ia+Kp+++i+ p ++v+ + + +tkgRhDpcv +ravp++Ea +a+vl+d++l lcl|NCBI__GCF_900141795.1:WP_074201084.1 278 VGGISTGQDIVAHIALKPTSSITVPGRSVTRNMEAVEMITKGRHDPCVGIRAVPIAEAQLAIVLMDHYL 346 *******************************998889999***************************** PP TIGR00033 346 ekras 350 ++ra+ lcl|NCBI__GCF_900141795.1:WP_074201084.1 347 RHRAQ 351 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (365 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: 11.58 // [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