Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate Ga0059261_2470 Ga0059261_2470 chorismate synthase (EC 4.2.3.5)
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__Korea:Ga0059261_2470 Length = 356 Score = 400 bits (1027), Expect = e-116 Identities = 204/357 (57%), Positives = 256/357 (71%), Gaps = 10/357 (2%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G++FR TT+GESHG A+G +VDG PPG+ LTEAD+Q LD+RRPG SR+TTQR+ Sbjct: 1 MSFNTFGRVFRFTTWGESHGPAIGAVVDGCPPGLALTEADIQPFLDKRRPGQSRFTTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPDQV+ILSGVFEG TTGT I L+IEN DQRS+DYS + +RPGHADY Y+ KYG RDY Sbjct: 61 EPDQVRILSGVFEGKTTGTPISLMIENVDQRSKDYSEVAAAYRPGHADYAYDAKYGFRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNPF 178 RGGGRSSARETA RVAAGA+A+ + + + I + +G +D D +++ NPF Sbjct: 121 RGGGRSSARETASRVAAGAVARAVIPD---VSILAWVEAIGGDAIDYAKFDAAEIGNNPF 177 Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238 FCPDPD ++L+ +K G S+GA + A+GVPAG G P++ +LD+++A A+MSIN Sbjct: 178 FCPDPDAAARWEKLVDDARKAGSSLGAVIACEATGVPAGWGAPLYAKLDSELAAAMMSIN 237 Query: 239 AVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQIIAHMALK 293 AVKGVEIGDGF AL G N D + K F +NHAGGI GGI++GQ + +A K Sbjct: 238 AVKGVEIGDGFAAAALSGEANADPMRPGNDGKPVFLANHAGGIAGGIATGQPVRVRVAFK 297 Query: 294 PTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350 PTSSI P TI R GE E+ TKGRHDPCVGIR VP+ EAM+A+VL D L RAQ Sbjct: 298 PTSSILTPVETITREGEATEIRTKGRHDPCVGIRGVPVVEAMMALVLADQKLLHRAQ 354 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: 423 Number of extensions: 17 Number of successful extensions: 4 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: 356 Length adjustment: 29 Effective length of query: 332 Effective length of database: 327 Effective search space: 108564 Effective search space used: 108564 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 Ga0059261_2470 Ga0059261_2470 (chorismate synthase (EC 4.2.3.5))
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.25710.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-137 442.9 0.0 4.2e-137 442.7 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2470 Ga0059261_2470 chorismate syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2470 Ga0059261_2470 chorismate synthase (EC 4.2.3.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.7 0.0 4.2e-137 4.2e-137 1 349 [. 10 353 .. 10 355 .. 0.97 Alignments for each domain: == domain 1 score: 442.7 bits; conditional E-value: 4.2e-137 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHg+a+ga++dG+P+gl lte+diq+ l++Rrpgqsr+t++r+E D+v+ilsGvfeGkTtG lcl|FitnessBrowser__Korea:Ga0059261_2470 10 FRFTTWGESHGPAIGAVVDGCPPGLALTEADIQPFLDKRRPGQSRFTTQRQEPDQVRILSGVFEGKTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+l+i+N d+rskdy++++ +RPgHady+y KYg++d++gggrsSaReTa rvaaGava++ + + lcl|FitnessBrowser__Korea:Ga0059261_2470 79 TPISLMIENVDQRSKDYSEVAAAYRPGHADYAYDAKYGFRDYRGGGRSSARETASRVAAGAVARAVIPD 147 ******************************************************************998 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 + i+a+v +g +++ +++ ++ ++p++cpd++a+++ e+++d a+k+g s+G+v+ + + lcl|FitnessBrowser__Korea:Ga0059261_2470 148 ---VSILAWVEAIGGDAIDYAKFD---AAEIGNNPFFCPDPDAAARWEKLVDDARKAGSSLGAVIACEA 210 ...88**********999965555...589999************************************ PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275 ++vp+g+G pl+ kld+ela+a++sinAvKgveiGdGF+aa G D++ d+k + +n+ GG lcl|FitnessBrowser__Korea:Ga0059261_2470 211 TGVPAGWGAPLYAKLDSELAAAMMSINAVKGVEIGDGFAAAALSGEANADPMRPGnDGKPVFLANHAGG 279 ****************************************************9877999********** PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344 i GGi++G+++rvr+a+Kp+++i +p +t++ e++ + +tkgRhDpcv +r vpvvEam+alvlad+ lcl|FitnessBrowser__Korea:Ga0059261_2470 280 IAGGIATGQPVRVRVAFKPTSSILTPVETITREGEATEIRTKGRHDPCVGIRGVPVVEAMMALVLADQK 348 ********************************988888888**************************99 PP TIGR00033 345 lekra 349 l +ra lcl|FitnessBrowser__Korea:Ga0059261_2470 349 LLHRA 353 98876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (356 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: 7.39 // [ok]
This GapMind analysis is from Apr 09 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