Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_050463059.1 AKL27_RS11980 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_001189915.1:WP_050463059.1 Length = 366 Score = 452 bits (1163), Expect = e-132 Identities = 222/359 (61%), Positives = 275/359 (76%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G LF VTTFGESHG A+GC++DG PPG+ L+EAD+Q +LDRR+PGTSR+ TQR+ Sbjct: 1 MSGNTFGTLFTVTTFGESHGPAIGCVIDGCPPGMVLSEADIQPELDRRKPGTSRHVTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD V+ILSGVFEG TTGT I LLI N DQRS+DY + + FRPGHADYTY KYG+RD Sbjct: 61 EPDTVEILSGVFEGKTTGTPIALLIRNQDQRSKDYGNLLETFRPGHADYTYWHKYGIRDP 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSAR TA V A A+AKK+L EK+G +GC++Q+GDI + + W V NPFF Sbjct: 121 RGGGRSSARLTAPVVGAAAVAKKWLFEKYGTTFKGCMSQLGDIAIPFESWEHVRDNPFFA 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 + I L+ M L+K GDS GA++ VVA VP GLGEP++D+LDA+IA+ALM INAV Sbjct: 181 ANASIIPQLESYMDDLRKVGDSCGARIDVVAQNVPVGLGEPIYDKLDAEIAYALMGINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF VA +G+++ DE+T GF N+AGGILGGIS+GQ+I A +A+KPTSSI Sbjct: 241 KGVEIGAGFKSVAQKGTEHGDELTPQGFIGNNAGGILGGISTGQEITASIAIKPTSSIRQ 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 ++I++ G+ ++ T GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQ DV D P Sbjct: 301 ARQSIDKAGQPSQVETFGRHDPCVGIRATPIAEAMLALVLMDHALRNRAQCGDVSVDTP 359 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: 435 Number of extensions: 14 Number of successful extensions: 1 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: 366 Length adjustment: 29 Effective length of query: 332 Effective length of database: 337 Effective search space: 111884 Effective search space used: 111884 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_050463059.1 AKL27_RS11980 (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.7182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-137 444.0 0.0 2e-137 443.8 0.0 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463059.1 AKL27_RS11980 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463059.1 AKL27_RS11980 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.8 0.0 2e-137 2e-137 1 349 [. 10 349 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 443.8 bits; conditional E-value: 2e-137 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++ttfGeSHg+a+g++idG+P+g+ l+e+diq+el+rR+pg+sr+ ++r+E D+veilsGvfeGkTtG lcl|NCBI__GCF_001189915.1:WP_050463059.1 10 FTVTTFGESHGPAIGCVIDGCPPGMVLSEADIQPELDRRKPGTSRHVTQRQEPDTVEILSGVFEGKTTG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pialli+N+d+rskdy ++ e++RPgHadyty++KYgi+d +gggrsSaR Ta v a avakk+L e lcl|NCBI__GCF_001189915.1:WP_050463059.1 79 TPIALLIRNQDQRSKDYGNLLETFRPGHADYTYWHKYGIRDPRGGGRSSARLTAPVVGAAAVAKKWLFE 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ++g+ ++ +++lg++++++e s e++ ++p+++++a+ ++e ++d ++k gds G++++vv+ lcl|NCBI__GCF_001189915.1:WP_050463059.1 148 KYGTTFKGCMSQLGDIAIPFE-----SWEHVRDNPFFAANASIIPQLESYMDDLRKVGDSCGARIDVVA 211 *******************84.....4567999************************************ PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 +nvpvglGep++dkldae+a+al++inAvKgveiG+GF+++ ++G e+ Del + + + nn GGi lcl|NCBI__GCF_001189915.1:WP_050463059.1 212 QNVPVGLGEPIYDKLDAEIAYALMGINAVKGVEIGAGFKSVAQKGTEHGDEL----TPQGFIGNNAGGI 276 **************************************************66....577899******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi++G++i+ +ia+Kp+++i+++++++d++++++ t gRhDpcv +ra+p++Eam+alvl+d++l lcl|NCBI__GCF_001189915.1:WP_050463059.1 277 LGGISTGQEITASIAIKPTSSIRQARQSIDKAGQPSQVETFGRHDPCVGIRATPIAEAMLALVLMDHAL 345 ********************************************************************* PP TIGR00033 346 ekra 349 ++ra lcl|NCBI__GCF_001189915.1:WP_050463059.1 346 RNRA 349 9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (366 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: 11.17 // [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