Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_019896127.1 A377_RS0109590 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000384235.1:WP_019896127.1 Length = 376 Score = 489 bits (1258), Expect = e-143 Identities = 236/359 (65%), Positives = 287/359 (79%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGN++GQ FRVTTFGESHG ALGCIVDG PPG+ L +D+Q +LDRR+PG ++ T RR Sbjct: 1 MAGNSLGQNFRVTTFGESHGPALGCIVDGCPPGLALDASDIQKELDRRKPGQIKHATARR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVFEG TTGT IGLLI NTDQRS+DYS + + FRP HADYTY QKYG RDY Sbjct: 61 EADEVEILSGVFEGKTTGTPIGLLIHNTDQRSKDYSKVAETFRPAHADYTYTQKYGFRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYL ++ G+EI+G L+Q+G I + W N +FC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLQQRLGVEIKGYLSQLGPIEIADVPWPFDNDNAYFC 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 P+ + + M L K+ DS+GAK+T++A VP GLGEPVFDRLDAD+AHALMSINAV Sbjct: 181 PNGARQAEISAYMDELMKQKDSVGAKITILAHQVPVGLGEPVFDRLDADLAHALMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIGDGF V A +G+++RDE+ DGF SNHAGGI+GGI++GQ I+A +ALKPTSSI Sbjct: 241 KGVEIGDGFAVAAQKGTEHRDELNPDGFASNHAGGIVGGIATGQDIVARIALKPTSSIMT 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 PG+++N E V+M+TKGRHDPCVG+RA PIAEA +AIV++DH LR RAQNADV +P Sbjct: 301 PGKSVNTRNESVDMVTKGRHDPCVGLRATPIAEAQMAIVILDHYLRHRAQNADVVPPMP 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: 484 Number of extensions: 16 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: 376 Length adjustment: 30 Effective length of query: 331 Effective length of database: 346 Effective search space: 114526 Effective search space used: 114526 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_019896127.1 A377_RS0109590 (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.30933.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-143 463.8 0.1 1.9e-143 463.6 0.1 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019896127.1 A377_RS0109590 chorismate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019896127.1 A377_RS0109590 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.6 0.1 1.9e-143 1.9e-143 1 350 [. 10 350 .. 10 351 .. 0.97 Alignments for each domain: == domain 1 score: 463.6 bits; conditional E-value: 1.9e-143 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHg+alg+i+dG+P+gl l+++diqkel+rR+pgq ++++ r+E+DeveilsGvfeGkTtG lcl|NCBI__GCF_000384235.1:WP_019896127.1 10 FRVTTFGESHGPALGCIVDGCPPGLALDASDIQKELDRRKPGQIKHATARREADEVEILSGVFEGKTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi lli+N+d+rskdy++++e++RP+Hadyty++KYg++d++gggrsSaReTa+rvaaGa+akk+L++ lcl|NCBI__GCF_000384235.1:WP_019896127.1 79 TPIGLLIHNTDQRSKDYSKVAETFRPAHADYTYTQKYGFRDYRGGGRSSARETAMRVAAGAIAKKYLQQ 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 g+ei++y+++lg +e+ + +++ +cp+ +++e+ +++d+++k++dsvG+++++++ lcl|NCBI__GCF_000384235.1:WP_019896127.1 148 RLGVEIKGYLSQLGPIEIADVPWPF-----DNDNAYFCPNGARQAEISAYMDELMKQKDSVGAKITILA 211 *******************877664.....344889********************************* PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++vpvglGep+fd+lda la+al+sinAvKgveiGdGF+ a ++G e+ Del+ + +n+ GGi lcl|NCBI__GCF_000384235.1:WP_019896127.1 212 HQVPVGLGEPVFDRLDADLAHALMSINAVKGVEIGDGFAVAAQKGTEHRDELN----PDGFASNHAGGI 276 **************************************************764....55799******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 GGi++G+di+ ria+Kp+++i +p k+v+++++ +tkgRhDpcv +ra+p++Ea +a+v++d++l lcl|NCBI__GCF_000384235.1:WP_019896127.1 277 VGGIATGQDIVARIALKPTSSIMTPGKSVNTRNESVDMVTKGRHDPCVGLRATPIAEAQMAIVILDHYL 345 *******************************999999999***************************** PP TIGR00033 346 ekras 350 ++ra+ lcl|NCBI__GCF_000384235.1:WP_019896127.1 346 RHRAQ 350 **987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (376 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: 8.66 // [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