Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate PP_1830 PP_1830 Chorismate synthase
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__Putida:PP_1830 Length = 363 Score = 518 bits (1334), Expect = e-152 Identities = 257/359 (71%), Positives = 303/359 (84%), Gaps = 1/359 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G+LF VTT GESHG AL IVDG PPG+ ++ ADLQHDLDRR+PGTSR+TTQR+ Sbjct: 1 MSGNTYGKLFTVTTAGESHGPALVAIVDGCPPGLEISLADLQHDLDRRKPGTSRHTTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVFEG TTG SIGLLI NTDQ+S+DYSAIKD+FRP HADYTY KYG+RDY Sbjct: 61 EADEVEILSGVFEGRTTGCSIGLLIRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKK+LA + GI +RG ++Q+G I + K W VEQN FF Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKFLATQ-GITVRGYMSQLGPIEIPFKTWESVEQNAFFS 179 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDPDK+ L+ M L+++ DS+GAK+TVVA GV GLGEP+FDRLDA++AHALMSINAV Sbjct: 180 PDPDKVPELEAYMDQLRRDQDSVGAKITVVAEGVMPGLGEPIFDRLDAELAHALMSINAV 239 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF VA RG+++RDE+T +GF SN+AGGILGGISSGQ I+AH+ALKPTSSIT Sbjct: 240 KGVEIGAGFASVAQRGTEHRDELTPEGFLSNNAGGILGGISSGQPIVAHLALKPTSSITT 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 PGR+I+ G V++ITKGRHDPCVGIRA PIAEAM+AI LMDHLLR RAQNADV+ + P Sbjct: 300 PGRSIDVDGNPVDVITKGRHDPCVGIRATPIAEAMMAIALMDHLLRHRAQNADVQVNTP 358 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: 478 Number of extensions: 13 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: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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 PP_1830 PP_1830 (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.4525.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-141 454.7 0.0 1.1e-140 454.5 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1830 PP_1830 Chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1830 PP_1830 Chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 454.5 0.0 1.1e-140 1.1e-140 1 350 [. 10 349 .. 10 350 .. 0.98 Alignments for each domain: == domain 1 score: 454.5 bits; conditional E-value: 1.1e-140 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiall 75 +++tt+GeSHg+al+ai+dG+P+gle++ +d+q++l+rR+pg+sr+t++r+E+DeveilsGvfeG+TtG i ll lcl|FitnessBrowser__Putida:PP_1830 10 FTVTTAGESHGPALVAIVDGCPPGLEISLADLQHDLDRRKPGTSRHTTQRQEADEVEILSGVFEGRTTGCSIGLL 84 789************************************************************************ PP TIGR00033 76 ikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvk 150 i+N+d++skdy+ ik+l+RP+Hadyty +KYgi+d++gggrsSaReTa+rvaaGa+akk+L+ +gi + +y+++ lcl|FitnessBrowser__Putida:PP_1830 85 IRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGIRDYRGGGRSSARETAMRVAAGAIAKKFLAT-QGITVRGYMSQ 158 **************************************************************9.99********* PP TIGR00033 151 lgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldae 225 lg +e++++ + e+++++ ++ pd+++ e+e+++d++++d+dsvG++++vv+++v glGep+fd+ldae lcl|FitnessBrowser__Putida:PP_1830 159 LGPIEIPFK-----TWESVEQNAFFSPDPDKVPELEAYMDQLRRDQDSVGAKITVVAEGVMPGLGEPIFDRLDAE 228 *******74.....45689******************************************************** PP TIGR00033 226 lasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikk 300 la+al+sinAvKgveiG+GF+++ +rG e+ Del+ + +nn GGi+GGi+ G++i+ + a+Kp+++i++ lcl|FitnessBrowser__Putida:PP_1830 229 LAHALMSINAVKGVEIGAGFASVAQRGTEHRDELTP----EGFLSNNAGGILGGISSGQPIVAHLALKPTSSITT 299 ********************************7754....479******************************** PP TIGR00033 301 plktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350 p +++d+++++ +tkgRhDpcv +ra+p++Eam+a+ l+d+ll++ra+ lcl|FitnessBrowser__Putida:PP_1830 300 PGRSIDVDGNPVDVITKGRHDPCVGIRATPIAEAMMAIALMDHLLRHRAQ 349 ***********************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (363 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.91 // [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