Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_010936239.1 DET_RS02505 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000011905.1:WP_010936239.1 Length = 364 Score = 254 bits (650), Expect = 2e-72 Identities = 147/353 (41%), Positives = 208/353 (58%), Gaps = 11/353 (3%) Query: 4 NTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRREPD 63 N++G+LF++T+FGESHG +G ++DGVP G+ + ++Q ++D+R+ + T R E D Sbjct: 3 NSLGKLFQITSFGESHGDCVGVVIDGVPAGLAINVDEIQVEVDKRKSRAKAHATPRCEDD 62 Query: 64 QVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKY-GLRDYRG 122 +++I SG+ TTG I L+I N + S +Y + RPGHAD+T KY G D+RG Sbjct: 63 RIEIFSGILNNFTTGAPICLVIWNKNIDSSEYERTRSKIRPGHADFTGFVKYGGFNDFRG 122 Query: 123 GGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDI---KDWSQ-VEQNPF 178 GGR S R TA V AGAIA+K L GIE+ G ++G I + KD Q + Q+ Sbjct: 123 GGRFSGRITAGHVMAGAIARK-LISTIGIEVIGYTAELGGIVAKLPKTKDIRQNISQSDV 181 Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238 CPD + L++ +EGDS+G V + +P GLGEPVFD L+ ++A A+ +I Sbjct: 182 NCPDLTATKKMLALIQQAAEEGDSLGGVVECLGLNLPVGLGEPVFDTLEGELAKAMFAIP 241 Query: 239 AVKGVEIGDGFDVVALRGSQNRDEITKDG----FQSNHAGGILGGISSGQQIIAHMALKP 294 AVKGVE G GF+ LRGS+N D + SN GG+LGGIS G + +A+KP Sbjct: 242 AVKGVEFGAGFEASRLRGSKNNDPFSIQANHIRTTSNKCGGVLGGISDGMPLQFRVAVKP 301 Query: 295 TSSITVPGRTIN-RFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLR 346 T SI++ T+N + +GRHD C+ RAV + EAM IVL D LR Sbjct: 302 TPSISLSQPTVNIDTMTNTSLEIRGRHDTCIVPRAVSVVEAMTCIVLADLALR 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: 331 Number of extensions: 13 Number of successful extensions: 7 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: 364 Length adjustment: 29 Effective length of query: 332 Effective length of database: 335 Effective search space: 111220 Effective search space used: 111220 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_010936239.1 DET_RS02505 (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.16368.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-129 417.5 0.3 2.4e-129 417.2 0.3 1.0 1 lcl|NCBI__GCF_000011905.1:WP_010936239.1 DET_RS02505 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000011905.1:WP_010936239.1 DET_RS02505 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.2 0.3 2.4e-129 2.4e-129 1 347 [. 9 355 .. 9 358 .. 0.98 Alignments for each domain: == domain 1 score: 417.2 bits; conditional E-value: 2.4e-129 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++t fGeSHg+ +g++idG+Pagl ++ ++iq e+++R+ ++++r E+D++ei sG+ + TtG lcl|NCBI__GCF_000011905.1:WP_010936239.1 9 FQITSFGESHGDCVGVVIDGVPAGLAINVDEIQVEVDKRKSRAKAHATPRCEDDRIEIFSGILNNFTTG 77 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarvaaGavakklLk 137 aPi+l+i Nk+++s++ye ++++ RPgHad+t+++KYg + +gggr S+R Ta++v+aGa+a+kl++ lcl|NCBI__GCF_000011905.1:WP_010936239.1 78 APICLVIWNKNIDSSEYERTRSKIRPGHADFTGFVKYGGFNdFRGGGRFSGRITAGHVMAGAIARKLIS 146 *************************************85544**************************9 PP TIGR00033 138 etagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevv 206 gie+++y+ +lg + ++ ++k+ +++++++s v+cpd +a+k+m ++i++a ++gds+Ggvve++ lcl|NCBI__GCF_000011905.1:WP_010936239.1 147 T-IGIEVIGYTAELGGIVAKLPKTKD-IRQNISQSDVNCPDLTATKKMLALIQQAAEEGDSLGGVVECL 213 9.89************9999877776.99**************************************** PP TIGR00033 207 vsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGG 275 n+pvglGep+fd l++ela+a+++i+AvKgve+G+GFea + rGs+ nD++ ++ ++ir+ +n++GG lcl|NCBI__GCF_000011905.1:WP_010936239.1 214 GLNLPVGLGEPVFDTLEGELAKAMFAIPAVKGVEFGAGFEASRLRGSKNNDPFSIQANHIRTTSNKCGG 282 ********************************************************************* PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvlada 343 ++GGi+ G+++++r+avKp+p+i+ + tv+++t+ +++ + +gRhD c+vprav vvEam+ +vlad+ lcl|NCBI__GCF_000011905.1:WP_010936239.1 283 VLGGISDGMPLQFRVAVKPTPSISLSQPTVNIDTMTNTSLEiRGRHDTCIVPRAVSVVEAMTCIVLADL 351 *****************************************9*************************** PP TIGR00033 344 llek 347 +l+ lcl|NCBI__GCF_000011905.1:WP_010936239.1 352 ALRA 355 9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (364 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: 7.26 // [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