Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_027180067.1 G496_RS0115510 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000429985.1:WP_027180067.1 Length = 349 Score = 355 bits (912), Expect = e-103 Identities = 182/348 (52%), Positives = 236/348 (67%), Gaps = 1/348 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G++F +TT+GESHG LG ++DG P GI LTE +Q +LDRR+PG T R+ Sbjct: 1 MSGNTFGKIFSLTTYGESHGPGLGGVIDGCPAGIALTEDIIQLELDRRKPGQGIAATARK 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+VK+LSG+FEG TTGT IG IENTD RS+DYS I DV+RPGHAD TY+ KYG+RDY Sbjct: 61 EADKVKLLSGIFEGRTTGTPIGFHIENTDHRSKDYSKIMDVYRPGHADLTYDAKYGVRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSS RET RV GA+A+++L + GI + +G I + D PFF Sbjct: 121 RGGGRSSGRETVSRVVGGAVAQEFL-KSSGISCQAYTVAIGGINAKVTDAEGAVNRPFFS 179 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PD I + ++ ++ +GD++G V + +GVPAGLGEPVFD+LDA +A+ALM + AV Sbjct: 180 PDDSIIPEWESKIKKVRSDGDTLGGVVEICLNGVPAGLGEPVFDKLDARLAYALMGVGAV 239 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF A GS N D + + GF+SN+AGGILGGISSGQQII +KP SI Sbjct: 240 KGVEIGSGFAASAATGSTNNDFMQQGGFKSNNAGGILGGISSGQQIIVRAHVKPIPSIAK 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348 +T+++ G EV + GRHD C R VP+ +AM + L D +L QR Sbjct: 300 EQQTVDKNGREVAISIGGRHDICAIPRIVPVLKAMAMLSLADFVLLQR 347 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: 377 Number of extensions: 17 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: 349 Length adjustment: 29 Effective length of query: 332 Effective length of database: 320 Effective search space: 106240 Effective search space used: 106240 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_027180067.1 G496_RS0115510 (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.32462.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-130 419.7 1.3 4.8e-130 419.5 1.3 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027180067.1 G496_RS0115510 chorismate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027180067.1 G496_RS0115510 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 419.5 1.3 4.8e-130 4.8e-130 1 348 [. 10 347 .. 10 349 .] 0.96 Alignments for each domain: == domain 1 score: 419.5 bits; conditional E-value: 4.8e-130 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 ++ltt+GeSHg+ lg +idG+Pag+ lte+ iq el+rR+pgq++ ++ rkE+D+v++lsG+feG+TtG lcl|NCBI__GCF_000429985.1:WP_027180067.1 10 FSLTTYGESHGPGLGGVIDGCPAGIALTEDIIQLELDRRKPGQGIAATARKEADKVKLLSGIFEGRTTG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi + i+N+d rskdy++i +++RPgHad+ty KYg++d++gggrsS+ReT+ rv+ Gava+++Lk+ lcl|NCBI__GCF_000429985.1:WP_027180067.1 79 TPIGFHIENTDHRSKDYSKIMDVYRPGHADLTYDAKYGVRDYRGGGRSSGRETVSRVVGGAVAQEFLKS 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +gi + ay+v +g ++++ + e + ++p++ pd + e e i+k+++dgd++Ggvve+ lcl|NCBI__GCF_000429985.1:WP_027180067.1 148 -SGISCQAYTVAIGGINAKVTD-----AEGAVNRPFFSPDDSIIPEWESKIKKVRSDGDTLGGVVEICL 210 .99*************999532.....3456669*********************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++vp+glGep+fdklda+la+al+++ AvKgveiG+GF+a +Gs nD + ++ +k+nn GGi lcl|NCBI__GCF_000429985.1:WP_027180067.1 211 NGVPAGLGEPVFDKLDARLAYALMGVGAVKGVEIGSGFAASAATGSTNNDFM----QQGGFKSNNAGGI 275 **************************************************33....34569******** PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G++i vr+ vKpip+i+k+++tvd++++e a gRhD c++pr+vpv am l lad +l lcl|NCBI__GCF_000429985.1:WP_027180067.1 276 LGGISSGQQIIVRAHVKPIPSIAKEQQTVDKNGREVAISIGGRHDICAIPRIVPVLKAMAMLSLADFVL 344 ***********************************99999**************************999 PP TIGR00033 346 ekr 348 +r lcl|NCBI__GCF_000429985.1:WP_027180067.1 345 LQR 347 775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (349 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: 7.05 // [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