Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_008803909.1 KVAR_RS06725 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000025465.1:WP_008803909.1 Length = 361 Score = 685 bits (1768), Expect = 0.0 Identities = 340/361 (94%), Positives = 347/361 (96%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR Sbjct: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDY AIKD+FRPGHADYTYEQKYGLRDY Sbjct: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYGAIKDLFRPGHADYTYEQKYGLRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYLA KFGI IRGCLTQMGDIPL IKDW QVEQNPFFC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLAAKFGIVIRGCLTQMGDIPLAIKDWDQVEQNPFFC 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDPDKIDALDELMR LKKEGDSIGAKVTVVA GVP GLGEPVFDRLDADIAHALMSINAV Sbjct: 181 PDPDKIDALDELMRGLKKEGDSIGAKVTVVADGVPPGLGEPVFDRLDADIAHALMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIGDGF+VV LRGS+NRDEITKDGFQSNHAGGILGGISSGQQI+A++ALKPTSSITV Sbjct: 241 KGVEIGDGFEVVKLRGSENRDEITKDGFQSNHAGGILGGISSGQQIVANIALKPTSSITV 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360 PG TINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDH +RQRAQN DV T IPR Sbjct: 301 PGHTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHFMRQRAQNGDVTTTIPR 360 Query: 361 W 361 W Sbjct: 361 W 361 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: 591 Number of extensions: 14 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: 361 Length adjustment: 29 Effective length of query: 332 Effective length of database: 332 Effective search space: 110224 Effective search space used: 110224 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_008803909.1 KVAR_RS06725 (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.30311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-142 458.4 0.1 8.2e-142 458.2 0.1 1.0 1 lcl|NCBI__GCF_000025465.1:WP_008803909.1 KVAR_RS06725 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025465.1:WP_008803909.1 KVAR_RS06725 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.2 0.1 8.2e-142 8.2e-142 1 350 [. 10 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 458.2 bits; conditional E-value: 8.2e-142 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHg alg+i+dG+P+g++lte+d+q++l+rRrpg+sr+t++r+E D+v+ilsGvfeG TtG lcl|NCBI__GCF_000025465.1:WP_008803909.1 10 FRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRREPDQVKILSGVFEGVTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 + i lli+N+d+rs+dy ik+l+RPgHadyty++KYg++d++gggrsSaReTa+rvaaGa+akk+L+ lcl|NCBI__GCF_000025465.1:WP_008803909.1 79 TSIGLLIENTDQRSQDYGAIKDLFRPGHADYTYEQKYGLRDYRGGGRSSARETAMRVAAGAIAKKYLAA 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 + gi i + ++++g++ l + + +++++p++cpd+++ +++ e++ +kk+gds+G++v+vv+ lcl|NCBI__GCF_000025465.1:WP_008803909.1 148 KFGIVIRGCLTQMGDIPLAIKDWD-----QVEQNPFFCPDPDKIDALDELMRGLKKEGDSIGAKVTVVA 211 ****************99965554.....79************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 +vp glGep+fd+lda +a+al+sinAvKgveiGdGFe ++ rGse De++ k +++n+ GGi lcl|NCBI__GCF_000025465.1:WP_008803909.1 212 DGVPPGLGEPVFDRLDADIAHALMSINAVKGVEIGDGFEVVKLRGSENRDEIT----KDGFQSNHAGGI 276 **************************************************875....45799******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G++i+ +ia+Kp+++i+ p +t++ ++e +tkgRhDpcv +ravp++Eam+a+vl+d+++ lcl|NCBI__GCF_000025465.1:WP_008803909.1 277 LGGISSGQQIVANIALKPTSSITVPGHTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHFM 345 ********************************************************************* PP TIGR00033 346 ekras 350 ++ra+ lcl|NCBI__GCF_000025465.1:WP_008803909.1 346 RQRAQ 350 *9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (361 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.09 // [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