Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011764770.1 AZO_RS05260 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000061505.1:WP_011764770.1 Length = 378 Score = 484 bits (1246), Expect = e-141 Identities = 234/360 (65%), Positives = 290/360 (80%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT+G LF VT+FGESHG A+GC++DG PPG+ LT AD+Q +LDRR+PGTSR+ TQRR Sbjct: 1 MSGNTLGTLFCVTSFGESHGPAIGCVIDGCPPGLSLTAADIQGELDRRKPGTSRHVTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD+V+ILSGVFEGVTTGT I LLI N DQRS+DY I + FRPGHADY Y QKYG+RDY Sbjct: 61 EPDEVEILSGVFEGVTTGTPIALLIRNQDQRSKDYGNIAETFRPGHADYPYWQKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETA+RVAAGA+A+K+L+E++GI IRG + Q+G +P+ W V NPFF Sbjct: 121 RGGGRSSARETAVRVAAGAVARKWLSERYGIVIRGYMAQLGPLPIPFVSWDAVGDNPFFA 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 P+ + + L+ M L+K GDS+GA++ VVASGVP G GEPV+DRLDADIA+A+MSINAV Sbjct: 181 PNAEIVPQLESYMDELRKSGDSVGARINVVASGVPVGWGEPVYDRLDADIAYAMMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF VA G+++ DE+T +GF SN+AGG+LGGISSGQ ++ MA+KPTSSI + Sbjct: 241 KGVEIGAGFASVAQLGTEHGDELTPEGFLSNNAGGVLGGISSGQDVLVSMAIKPTSSIRL 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360 R+I+R G V + T GRHDPCVGIRA P+AEAMLA+VLMDH LR RAQ DV+T P+ Sbjct: 301 DRRSIDREGNPVIVNTHGRHDPCVGIRATPVAEAMLALVLMDHALRHRAQCGDVRTATPQ 360 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: 468 Number of extensions: 10 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: 378 Length adjustment: 30 Effective length of query: 331 Effective length of database: 348 Effective search space: 115188 Effective search space used: 115188 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_011764770.1 AZO_RS05260 (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.25361.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-140 453.9 0.0 2e-140 453.7 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764770.1 AZO_RS05260 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764770.1 AZO_RS05260 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.7 0.0 2e-140 2e-140 2 350 .. 11 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 453.7 bits; conditional E-value: 2e-140 TIGR00033 2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 +t fGeSHg+a+g++idG+P+gl+lt++diq el+rR+pg+sr+ ++r+E DeveilsGvfeG TtG+ lcl|NCBI__GCF_000061505.1:WP_011764770.1 11 CVTSFGESHGPAIGCVIDGCPPGLSLTAADIQGELDRRKPGTSRHVTQRREPDEVEILSGVFEGVTTGT 79 6899***************************************************************** PP TIGR00033 71 PiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLket 139 Pialli+N+d+rskdy +i+e++RPgHady y++KYgi+d++gggrsSaReTa+rvaaGava+k+L+e lcl|NCBI__GCF_000061505.1:WP_011764770.1 80 PIALLIRNQDQRSKDYGNIAETFRPGHADYPYWQKYGIRDYRGGGRSSARETAVRVAAGAVARKWLSER 148 ********************************************************************* PP TIGR00033 140 agieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvs 208 +gi i +y+ +lg + +++ s + ++ ++p+++p+ae ++e ++d+++k+gdsvG++++vv+s lcl|NCBI__GCF_000061505.1:WP_011764770.1 149 YGIVIRGYMAQLGPLPIPFVSWD-----AVGDNPFFAPNAEIVPQLESYMDELRKSGDSVGARINVVAS 212 ******************85555.....6999************************************* PP TIGR00033 209 nvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGie 277 +vpvg+Gep++d+lda +a+a++sinAvKgveiG+GF+++ + G e+ Del+ + +nn GG++ lcl|NCBI__GCF_000061505.1:WP_011764770.1 213 GVPVGWGEPVYDRLDADIAYAMMSINAVKGVEIGAGFASVAQLGTEHGDELTP----EGFLSNNAGGVL 277 *************************************************7754....479********* PP TIGR00033 278 GGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladalle 346 GGi+ G+d+ v++a+Kp+++i+ +++++d e+++ + t+gRhDpcv +ra+pv+Eam+alvl+d++l+ lcl|NCBI__GCF_000061505.1:WP_011764770.1 278 GGISSGQDVLVSMAIKPTSSIRLDRRSIDREGNPVIVNTHGRHDPCVGIRATPVAEAMLALVLMDHALR 346 ********************************************************************* PP TIGR00033 347 kras 350 +ra+ lcl|NCBI__GCF_000061505.1:WP_011764770.1 347 HRAQ 350 9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (378 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.66 // [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