Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_093396091.1 BM091_RS12045 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_900114975.1:WP_093396091.1 Length = 357 Score = 385 bits (990), Expect = e-112 Identities = 194/345 (56%), Positives = 248/345 (71%), Gaps = 1/345 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGNT G++FRVTT+GESHG ALG ++DG PPG+ L+E D+Q DLDRRRPG S +T+R+ Sbjct: 1 MAGNTFGKMFRVTTWGESHGKALGAVIDGCPPGLSLSEEDIQKDLDRRRPGRSPASTKRK 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVFEG TTGT I L+I N D RS DYS + D +RPGHAD TYEQKYGLRD+ Sbjct: 61 ESDRVQILSGVFEGKTTGTPISLIIYNEDARSGDYSTLADTYRPGHADRTYEQKYGLRDW 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARET RVAAGA+A+K+L+ FGI + ++ + + D + ++ NPF+C Sbjct: 121 RGGGRSSARETVARVAAGAVARKFLS-TFGINVVAYTLELAGVKCNRIDETVIDNNPFYC 179 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PD + + + +++ GDS G V VVA G P GLGEPVFD+LDA IA+ALMSI AV Sbjct: 180 PDEEAAQLMAVKIDEIRRRGDSCGGIVQVVARGCPPGLGEPVFDKLDARIAYALMSIGAV 239 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF + GS++ D IT +G+ SN+AGGILGGISSG I+A +A+KP SI + Sbjct: 240 KGVEIGSGFRCARMLGSEHNDPITPEGYASNNAGGILGGISSGMDIVARVAVKPIPSIRI 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLL 345 +TI R G + KGRHD R VP+ EAM+ +VL D +L Sbjct: 300 AQQTITRDGRPTTITVKGRHDVSAIPRIVPVCEAMMLLVLADFML 344 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: 399 Number of extensions: 11 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: 357 Length adjustment: 29 Effective length of query: 332 Effective length of database: 328 Effective search space: 108896 Effective search space used: 108896 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_093396091.1 BM091_RS12045 (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.19855.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-141 457.3 0.0 1.8e-141 457.1 0.0 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093396091.1 BM091_RS12045 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093396091.1 BM091_RS12045 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.1 0.0 1.8e-141 1.8e-141 1 346 [. 10 345 .. 10 350 .. 0.97 Alignments for each domain: == domain 1 score: 457.1 bits; conditional E-value: 1.8e-141 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHgkalga+idG+P+gl+l+eediqk+l+rRrpg s +++rkE+D+v+ilsGvfeGkTtG lcl|NCBI__GCF_900114975.1:WP_093396091.1 10 FRVTTWGESHGKALGAVIDGCPPGLSLSEEDIQKDLDRRRPGRSPASTKRKESDRVQILSGVFEGKTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+l+i+N+d rs dy+ +++++RPgHad ty++KYg++d +gggrsSaReT+arvaaGava+k+L+ lcl|NCBI__GCF_900114975.1:WP_093396091.1 79 TPISLIIYNEDARSGDYSTLADTYRPGHADRTYEQKYGLRDWRGGGRSSARETVARVAAGAVARKFLST 147 ********************************************************************9 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 gi++vay+ +l+ v++++ i + +d++p+ cpd+ea++ m id++++ gds Gg+v+vv+ lcl|NCBI__GCF_900114975.1:WP_093396091.1 148 -FGINVVAYTLELAGVKCNR-----IDETVIDNNPFYCPDEEAAQLMAVKIDEIRRRGDSCGGIVQVVA 210 .88***************96.....456789************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++ p glGep+fdklda++a+al+si AvKgveiG+GF+ a++ Gse+nD+++ e +nn GGi lcl|NCBI__GCF_900114975.1:WP_093396091.1 211 RGCPPGLGEPVFDKLDARIAYALMSIGAVKGVEIGSGFRCARMLGSEHNDPITPE----GYASNNAGGI 275 **************************************************99765....4689****** PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+di+ r+avKpip+i+ +++t++ ++++++ + kgRhD++++pr+vpv+Eam+ lvlad +l lcl|NCBI__GCF_900114975.1:WP_093396091.1 276 LGGISSGMDIVARVAVKPIPSIRIAQQTITRDGRPTTITVKGRHDVSAIPRIVPVCEAMMLLVLADFML 344 *******************************999999999***************************99 PP TIGR00033 346 e 346 + lcl|NCBI__GCF_900114975.1:WP_093396091.1 345 H 345 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (357 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.64 // [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