Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate Pf6N2E2_5822 Chorismate synthase (EC 4.2.3.5)
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 Length = 363 Score = 518 bits (1334), Expect = e-152 Identities = 258/359 (71%), Positives = 300/359 (83%), Gaps = 1/359 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G+LF VTT GESHG AL IVDG PPG+ ++ DLQ DLDRR+PGTSR+TTQR+ Sbjct: 1 MSGNTYGKLFTVTTAGESHGPALVAIVDGCPPGLEISLDDLQRDLDRRKPGTSRHTTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVFEG TTG +IGLLI NTDQ+S+DYSAIKD+FRP HADYTY KYG RDY Sbjct: 61 EADEVEILSGVFEGRTTGCAIGLLIRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGERDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYLA + GI IRG ++Q+G I + K W VEQN FFC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLASQ-GIVIRGYMSQLGPIEIPFKTWDSVEQNAFFC 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 DGF SN+AGGILGGISSGQ I+AH+ALKPTSSIT Sbjct: 240 KGVEIGAGFACVAQRGTEHRDELTPDGFLSNNAGGILGGISSGQPIVAHLALKPTSSITT 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 PGR+I+ G V++ITKGRHDPCVGIRA PIAEAM+AIVLMDHLLR R QNADV+ P Sbjct: 300 PGRSIDIHGNPVDVITKGRHDPCVGIRATPIAEAMMAIVLMDHLLRHRGQNADVRVSTP 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: 477 Number of extensions: 18 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 Pf6N2E2_5822 (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.4527.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-142 458.5 0.0 7.6e-142 458.3 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 Chorismate synthase (EC 4.2.3.5) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 Chorismate synthase (EC 4.2.3.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.3 0.0 7.6e-142 7.6e-142 1 350 [. 10 349 .. 10 350 .. 0.98 Alignments for each domain: == domain 1 score: 458.3 bits; conditional E-value: 7.6e-142 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe 64 +++tt+GeSHg+al+ai+dG+P+gle++ +d+q++l+rR+pg+sr+t++r+E+DeveilsGvfe lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 10 FTVTTAGESHGPALVAIVDGCPPGLEISLDDLQRDLDRRKPGTSRHTTQRQEADEVEILSGVFE 73 789************************************************************* PP TIGR00033 65 GkTtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaa 128 G+TtG i lli+N+d++skdy+ ik+l+RP+Hadyty +KYg +d++gggrsSaReTa+rvaa lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 74 GRTTGCAIGLLIRNTDQKSKDYSAIKDLFRPAHADYTYHHKYGERDYRGGGRSSARETAMRVAA 137 **************************************************************** PP TIGR00033 129 GavakklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidka 192 Ga+akk+L++ +gi i +y+++lg +e+++++ + +++++ ++cpd+++ e+e+++d++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 138 GAIAKKYLAS-QGIVIRGYMSQLGPIEIPFKTWD-----SVEQNAFFCPDPDKVPELEAYMDQL 195 **********.99****************86665.....6999********************* PP TIGR00033 193 kkdgdsvGgvvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGsean 256 ++d+dsvG++++vv+++v glGep+fd+ldaela+al+sinAvKgveiG+GF+ + +rG e+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 196 RRDQDSVGAKITVVAEGVMPGLGEPIFDRLDAELAHALMSINAVKGVEIGAGFACVAQRGTEHR 259 **************************************************************** PP TIGR00033 257 DelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRh 320 Del+ + +nn GGi+GGi+ G++i+ + a+Kp+++i++p +++d+++++ +tkgRh lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 260 DELTP----DGFLSNNAGGILGGISSGQPIVAHLALKPTSSITTPGRSIDIHGNPVDVITKGRH 319 *7654....4699*************************************************** PP TIGR00033 321 DpcvvpravpvvEamvalvladallekras 350 Dpcv +ra+p++Eam+a+vl+d+ll++r++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5822 320 DPCVGIRATPIAEAMMAIVLMDHLLRHRGQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.76 // [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