Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_084056499.1 B9A12_RS03920 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_900176285.1:WP_084056499.1 Length = 352 Score = 392 bits (1006), Expect = e-113 Identities = 195/345 (56%), Positives = 251/345 (72%), Gaps = 2/345 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GN+ G+LFRV T+GESHG ALG ++DG PPGIPL+E D+Q DL+RRRPG + TT RR Sbjct: 1 MSGNSFGRLFRVMTWGESHGPALGAVIDGCPPGIPLSEEDIQKDLERRRPG-KKLTTARR 59 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD+V+ILSGVFEGVTTGT I L+I N D RS+DY A+KDV+RPGHAD TYEQKYG+RD+ Sbjct: 60 EPDEVRILSGVFEGVTTGTPISLVIFNKDVRSRDYEALKDVYRPGHADRTYEQKYGVRDW 119 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSS RET RVAAGA+A+K+L+++ GI + +GD+ + DW +NP FC Sbjct: 120 RGGGRSSGRETVARVAAGAVARKFLSQE-GIRVFAGTVALGDVTCRVHDWEAAAENPLFC 178 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDP+ A+++ ++ ++ +GD++G V V A G P GLGEPVFD+LDA +A ALMSI AV Sbjct: 179 PDPEAARAMEKQLQEVRAQGDTLGGIVQVNAVGCPPGLGEPVFDKLDARLAAALMSIGAV 238 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF + GS+N D T DG+ SN+AGG+LGGISSG ++ A+KP SI Sbjct: 239 KGVEIGAGFASACMLGSENNDTPTADGYASNNAGGVLGGISSGMDLVVRAAVKPIPSIAK 298 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLL 345 RT+ R G+E + GRHD R VP+ EAM+ I L D +L Sbjct: 299 EQRTVTRDGKETCLRIGGRHDIAAIPRIVPVCEAMVLITLADFML 343 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: 397 Number of extensions: 16 Number of successful extensions: 3 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: 352 Length adjustment: 29 Effective length of query: 332 Effective length of database: 323 Effective search space: 107236 Effective search space used: 107236 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_084056499.1 B9A12_RS03920 (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.31178.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-135 436.9 0.0 3.1e-135 436.6 0.0 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084056499.1 B9A12_RS03920 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084056499.1 B9A12_RS03920 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.6 0.0 3.1e-135 3.1e-135 1 346 [. 10 344 .. 10 348 .. 0.97 Alignments for each domain: == domain 1 score: 436.6 bits; conditional E-value: 3.1e-135 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r++t+GeSHg+alga+idG+P+g++l+eediqk+l+rRrpg+ +lt+ r+E Dev+ilsGvfeG TtG lcl|NCBI__GCF_900176285.1:WP_084056499.1 10 FRVMTWGESHGPALGAVIDGCPPGIPLSEEDIQKDLERRRPGK-KLTTARREPDEVRILSGVFEGVTTG 77 89*****************************************.9************************ PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+l+i Nkdvrs+dye +k+++RPgHad ty++KYg++d +gggrsS+ReT+arvaaGava+k+L++ lcl|NCBI__GCF_900176285.1:WP_084056499.1 78 TPISLVIFNKDVRSRDYEALKDVYRPGHADRTYEQKYGVRDWRGGGRSSGRETVARVAAGAVARKFLSQ 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +gi++ a +v lg+v+++ + e+++++p++cpd+ea+++me+++++++ +gd++Gg+v+v + lcl|NCBI__GCF_900176285.1:WP_084056499.1 147 -EGIRVFAGTVALGDVTCRVHD-----WEAAAENPLFCPDPEAARAMEKQLQEVRAQGDTLGGIVQVNA 209 .89****************633.....467889************************************ PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 + p glGep+fdklda+la+al+si AvKgveiG+GF++a + Gse nD + + +nn GG+ lcl|NCBI__GCF_900176285.1:WP_084056499.1 210 VGCPPGLGEPVFDKLDARLAAALMSIGAVKGVEIGAGFASACMLGSENND----TPTADGYASNNAGGV 274 **************************************************....55566678******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+d++vr+avKpip+i+k+++tv+ ++ke+ + gRhD +++pr+vpv+Eamv ++lad +l lcl|NCBI__GCF_900176285.1:WP_084056499.1 275 LGGISSGMDLVVRAAVKPIPSIAKEQRTVTRDGKETCLRIGGRHDIAAIPRIVPVCEAMVLITLADFML 343 ******************************************************************999 PP TIGR00033 346 e 346 + lcl|NCBI__GCF_900176285.1:WP_084056499.1 344 H 344 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (352 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: 00:00:00.01 # Mc/sec: 9.91 // [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