Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013819294.1 METME_RS13460 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000214665.1:WP_013819294.1 Length = 362 Score = 538 bits (1387), Expect = e-158 Identities = 261/359 (72%), Positives = 307/359 (85%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT+G+LF VTTFGESHG ALG IVDG PPG+ L+EADLQ DLDRR+PGTSR+TTQRR Sbjct: 1 MSGNTLGKLFTVTTFGESHGPALGAIVDGCPPGMELSEADLQIDLDRRKPGTSRHTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+VKILSGVFEG TTG IGLLIENTDQRS+DYS I + FRPGHADYTY+QKYG RDY Sbjct: 61 EADEVKILSGVFEGKTTGCPIGLLIENTDQRSKDYSKIAESFRPGHADYTYQQKYGFRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYL E+ GI++RG L+Q+G I ++ DW ++ NPFFC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLFEQHGIQVRGYLSQLGPIKIEGFDWDEIGNNPFFC 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PD K+ ++ M AL+KEG+SIGAK+ V+A VP GLGEP+FDRLDAD+AHALMSINAV Sbjct: 181 PDASKVAEMERYMDALRKEGESIGAKIEVIAGNVPPGLGEPIFDRLDADLAHALMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIGDGFD + +G+Q RDEIT +GF SNHAGGILGGISSGQ I+A MALKPTSS+ + Sbjct: 241 KGVEIGDGFDCIDTKGTQFRDEITPEGFLSNHAGGILGGISSGQDIVARMALKPTSSLRL 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 PGR+IN GE +E++T+GRHDPCVGIRA PIAEAM+AIVLMDHLLR R+QN V++ +P Sbjct: 301 PGRSINVHGEPIEVVTEGRHDPCVGIRATPIAEAMMAIVLMDHLLRHRSQNLHVQSGLP 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: 506 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: 362 Length adjustment: 29 Effective length of query: 332 Effective length of database: 333 Effective search space: 110556 Effective search space used: 110556 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_013819294.1 METME_RS13460 (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.4903.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-144 466.4 0.0 3e-144 466.2 0.0 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013819294.1 METME_RS13460 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013819294.1 METME_RS13460 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.2 0.0 3e-144 3e-144 1 350 [. 10 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 466.2 bits; conditional E-value: 3e-144 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++ttfGeSHg+algai+dG+P+g+el+e+d+q +l+rR+pg+sr+t++r+E+Dev+ilsGvfeGkTtG lcl|NCBI__GCF_000214665.1:WP_013819294.1 10 FTVTTFGESHGPALGAIVDGCPPGMELSEADLQIDLDRRKPGTSRHTTQRREADEVKILSGVFEGKTTG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 Pi lli+N+d+rskdy++i+e++RPgHadyty++KYg++d++gggrsSaReTa+rvaaGa+akk+L e lcl|NCBI__GCF_000214665.1:WP_013819294.1 79 CPIGLLIENTDQRSKDYSKIAESFRPGHADYTYQQKYGFRDYRGGGRSSARETAMRVAAGAIAKKYLFE 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ++gi++ +y+++lg +++e + ++ ++p++cpda++ +eme ++d ++k+g+s+G+++ev++ lcl|NCBI__GCF_000214665.1:WP_013819294.1 148 QHGIQVRGYLSQLGPIKIEGFDWD-----EIGNNPFFCPDASKVAEMERYMDALRKEGESIGAKIEVIA 211 *******************75444.....6999************************************ PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 nvp glGep+fd+lda la+al+sinAvKgveiGdGF+ ++G + De++ e + +n+ GGi lcl|NCBI__GCF_000214665.1:WP_013819294.1 212 GNVPPGLGEPIFDRLDADLAHALMSINAVKGVEIGDGFDCIDTKGTQFRDEITPE----GFLSNHAGGI 276 **************************************************88655....69******** PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+di+ r+a+Kp+++++ p +++++++++ +t+gRhDpcv +ra+p++Eam+a+vl+d+ll lcl|NCBI__GCF_000214665.1:WP_013819294.1 277 LGGISSGQDIVARMALKPTSSLRLPGRSINVHGEPIEVVTEGRHDPCVGIRATPIAEAMMAIVLMDHLL 345 *******************************999999999***************************** PP TIGR00033 346 ekras 350 ++r++ lcl|NCBI__GCF_000214665.1:WP_013819294.1 346 RHRSQ 350 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (362 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: 7.88 // [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