Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_078717330.1 B5D49_RS08820 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_900167125.1:WP_078717330.1 Length = 355 Score = 363 bits (931), Expect = e-105 Identities = 183/350 (52%), Positives = 241/350 (68%), Gaps = 3/350 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GN G+LFR+TT+GESHG LG ++DG P G+PL EA +Q DLD RRPG +T R+ Sbjct: 1 MSGNVFGELFRLTTYGESHGPGLGGVIDGCPAGVPLNEAMIQADLDLRRPGKGPASTARQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D V++LSGVFEGVTTGT I + N DQRS+DYS IKDVFRPGHAD+ + K+G+RDY Sbjct: 61 EADAVRLLSGVFEGVTTGTPIAFHVANQDQRSRDYSDIKDVFRPGHADFGFHAKFGVRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIP--LDIKDWSQVEQNPF 178 RGGGRSS RET RVA GA+A + LA + GI ++ ++G +P DW + PF Sbjct: 121 RGGGRSSGRETVSRVAGGAVAAQLLALE-GISVQARTVELGGLPPVAGEVDWDTTREMPF 179 Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238 F P P + ++ +R +K++GD++G V + A GVP GLGEPVF +LDA +A ALMS+ Sbjct: 180 FAPGPQTAEQWEQRIRDVKRQGDTLGGVVEIRAQGVPPGLGEPVFGKLDARLAGALMSVG 239 Query: 239 AVKGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSI 298 AVKGVEIG+GF L GSQN D +T GF SN +GG+LGGI+SGQ ++A +A+KP SI Sbjct: 240 AVKGVEIGEGFAAARLLGSQNNDPMTSKGFASNKSGGVLGGIASGQDVLARVAVKPIPSI 299 Query: 299 TVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348 + RT+N G+E + GRHD R VP+ AM+++VL D +L R Sbjct: 300 ALEQRTVNSAGKEATIRIGGRHDISAIPRIVPVLRAMVSLVLADLILLDR 349 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: 412 Number of extensions: 15 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: 355 Length adjustment: 29 Effective length of query: 332 Effective length of database: 326 Effective search space: 108232 Effective search space used: 108232 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_078717330.1 B5D49_RS08820 (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.29759.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-126 407.0 0.0 3.9e-126 406.7 0.0 1.0 1 lcl|NCBI__GCF_900167125.1:WP_078717330.1 B5D49_RS08820 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900167125.1:WP_078717330.1 B5D49_RS08820 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.7 0.0 3.9e-126 3.9e-126 1 346 [. 10 347 .. 10 351 .. 0.97 Alignments for each domain: == domain 1 score: 406.7 bits; conditional E-value: 3.9e-126 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +rltt+GeSHg+ lg +idG+Pag++l+e++iq +l+ Rrpg++ ++ r+E+D+v++lsGvfeG TtG lcl|NCBI__GCF_900167125.1:WP_078717330.1 10 FRLTTYGESHGPGLGGVIDGCPAGVPLNEAMIQADLDLRRPGKGPASTARQEADAVRLLSGVFEGVTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pia+ + N+d+rs+dy+dik+++RPgHad+ K+g++d++gggrsS+ReT+ rva Gava +lL+ lcl|NCBI__GCF_900167125.1:WP_078717330.1 79 TPIAFHVANQDQRSRDYSDIKDVFRPGHADFGFHAKFGVRDYRGGGRSSGRETVSRVAGGAVAAQLLAL 147 ********************************************************************9 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +gi + a +v+lg + +++ +++ + p+++p ++++++ e+ i +k++gd++Ggvve+ + lcl|NCBI__GCF_900167125.1:WP_078717330.1 148 -EGISVQARTVELGGLPPVAGEVD---WDTTREMPFFAPGPQTAEQWEQRIRDVKRQGDTLGGVVEIRA 212 .89************988765555...4667779*********************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++vp glGep+f klda+la al+s+ AvKgveiG+GF+aa+ Gs+ nD+++ + +n+sGG+ lcl|NCBI__GCF_900167125.1:WP_078717330.1 213 QGVPPGLGEPVFGKLDARLAGALMSVGAVKGVEIGEGFAAARLLGSQNNDPMTS----KGFASNKSGGV 277 **************************************************9975....4799******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+d+ r+avKpip+i+ +++tv+ ++ke++ + gRhD +++pr+vpv amv+lvlad++l lcl|NCBI__GCF_900167125.1:WP_078717330.1 278 LGGIASGQDVLARVAVKPIPSIALEQRTVNSAGKEATIRIGGRHDISAIPRIVPVLRAMVSLVLADLIL 346 *******************************************************************98 PP TIGR00033 346 e 346 lcl|NCBI__GCF_900167125.1:WP_078717330.1 347 L 347 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (355 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: 7.64 // [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