Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_077277921.1 B1C78_RS03730 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_002000365.1:WP_077277921.1 Length = 366 Score = 533 bits (1372), Expect = e-156 Identities = 260/359 (72%), Positives = 304/359 (84%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G+LF VT+FGESHG A+GCIVDG PPG+ L EADLQ DL+RRRPG SR+TTQRR Sbjct: 1 MSGNTTGKLFTVTSFGESHGAAIGCIVDGCPPGMALCEADLQPDLERRRPGKSRHTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E DQV+ILSGVFEGVTTGT I L+IEN DQRS+DYS I D FRPGHADYTY +KYGLRDY Sbjct: 61 ETDQVRILSGVFEGVTTGTPIALMIENVDQRSKDYSNIADRFRPGHADYTYFKKYGLRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAGAIAKKYL E++G+EIRG L Q+G I + KDW VEQNPFFC Sbjct: 121 RGGGRSSARETAMRVAAGAIAKKYLRERYGVEIRGYLAQLGPIVTEHKDWDAVEQNPFFC 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PD DK+ L+ M AL+KEG+S+GA++ VVA+GVP G GEP+FDRLDADIAHA+M+INAV Sbjct: 181 PDADKVAELEAYMDALRKEGNSVGARINVVATGVPPGWGEPIFDRLDADIAHAMMAINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIGDGF V+ +G+++RDE+T +GF SNH+GG LGGISSGQ I +ALKPTSSI + Sbjct: 241 KGVEIGDGFASVSQKGTEHRDEMTPEGFLSNHSGGTLGGISSGQDIRVSIALKPTSSIRL 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIP 359 PGRT+N GE VE++T GRHDPCVGIRA PIAEA LA+VLMDH LR RAQ DV+T++P Sbjct: 301 PGRTVNVKGEPVEVVTTGRHDPCVGIRATPIAEAALAVVLMDHALRHRAQCGDVRTEMP 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: 487 Number of extensions: 11 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: 366 Length adjustment: 29 Effective length of query: 332 Effective length of database: 337 Effective search space: 111884 Effective search space used: 111884 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_077277921.1 B1C78_RS03730 (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.20336.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-146 472.1 0.0 5.6e-146 471.9 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077277921.1 B1C78_RS03730 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077277921.1 B1C78_RS03730 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.9 0.0 5.6e-146 5.6e-146 1 350 [. 10 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 471.9 bits; conditional E-value: 5.6e-146 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++t fGeSHg+a+g+i+dG+P+g+ l e+d+q++l+rRrpg+sr+t++r+E+D+v+ilsGvfeG TtG lcl|NCBI__GCF_002000365.1:WP_077277921.1 10 FTVTSFGESHGAAIGCIVDGCPPGMALCEADLQPDLERRRPGKSRHTTQRRETDQVRILSGVFEGVTTG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pial+i+N d+rskdy++i++++RPgHadyty+kKYg++d++gggrsSaReTa+rvaaGa+akk+L+e lcl|NCBI__GCF_002000365.1:WP_077277921.1 79 TPIALMIENVDQRSKDYSNIADRFRPGHADYTYFKKYGLRDYRGGGRSSARETAMRVAAGAIAKKYLRE 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +g+ei +y+ +lg + +e++ + +++++p++cpda++ +e+e+++d ++k+g+svG++++vv+ lcl|NCBI__GCF_002000365.1:WP_077277921.1 148 RYGVEIRGYLAQLGPIVTEHKDWD-----AVEQNPFFCPDADKVAELEAYMDALRKEGNSVGARINVVA 211 ***************999986665.....69************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++vp g+Gep+fd+lda +a+a+++inAvKgveiGdGF+++s++G e+ De++ e + +n+sGG+ lcl|NCBI__GCF_002000365.1:WP_077277921.1 212 TGVPPGWGEPIFDRLDADIAHAMMAINAVKGVEIGDGFASVSQKGTEHRDEMTPE----GFLSNHSGGT 276 **************************************************88654....69******** PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+dirv+ia+Kp+++i+ p +tv++++++ +t+gRhDpcv +ra+p++Ea++a+vl+d++l lcl|NCBI__GCF_002000365.1:WP_077277921.1 277 LGGISSGQDIRVSIALKPTSSIRLPGRTVNVKGEPVEVVTTGRHDPCVGIRATPIAEAALAVVLMDHAL 345 *******************************999999999***************************** PP TIGR00033 346 ekras 350 ++ra+ lcl|NCBI__GCF_002000365.1:WP_077277921.1 346 RHRAQ 350 *9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (366 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.51 // [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