Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate Dsui_3204 Dsui_3204 chorismate synthase
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__PS:Dsui_3204 Length = 368 Score = 474 bits (1221), Expect = e-138 Identities = 234/360 (65%), Positives = 285/360 (79%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT G LF VT+FGESHG A+GC+VDG PPG+ LTEAD+Q +LDRR+PGTSR+ TQRR Sbjct: 1 MSGNTFGTLFTVTSFGESHGPAIGCVVDGCPPGLELTEADIQAELDRRKPGTSRHVTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD V+ILSGVFEG TTGT IGLLI N DQRS+DY I FRPGHADY Y QKYG RDY Sbjct: 61 EPDTVEILSGVFEGKTTGTPIGLLIRNQDQRSKDYGNIASTFRPGHADYGYTQKYGFRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETA+RVAAGAIA+K+L +++GI IRG ++Q+G I + D + ++ N FF Sbjct: 121 RGGGRSSARETAVRVAAGAIARKWLQQRYGISIRGWMSQLGPIEIPFVDAAAIDGNAFFA 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 P+ + L+ M AL+K DS+GAK+TV A+GVP G GEPV+DRLDA+IA+A+M INAV Sbjct: 181 PNAAIVPELEAYMDALRKSLDSVGAKITVTATGVPPGWGEPVYDRLDAEIAYAMMGINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF +A +GS++ DE+T GF SNHAGG+LGGIS+GQ I+ +MA+KPTSSI Sbjct: 241 KGVEIGAGFASIAQKGSEHGDEMTPAGFLSNHAGGVLGGISTGQDIVVNMAIKPTSSIAQ 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360 P R+++ G VE+ T+GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQ DV PR Sbjct: 301 PRRSVDVQGNAVEVATEGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQCGDVVCATPR 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: 449 Number of extensions: 9 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: 368 Length adjustment: 29 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 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 Dsui_3204 Dsui_3204 (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.24958.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-143 461.5 0.1 9.5e-143 461.3 0.1 1.0 1 lcl|FitnessBrowser__PS:Dsui_3204 Dsui_3204 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3204 Dsui_3204 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.3 0.1 9.5e-143 9.5e-143 1 350 [. 10 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 461.3 bits; conditional E-value: 9.5e-143 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiallik 77 +++t fGeSHg+a+g+++dG+P+glelte+diq el+rR+pg+sr+ ++r+E D+veilsGvfeGkTtG+Pi lli+ lcl|FitnessBrowser__PS:Dsui_3204 10 FTVTSFGESHGPAIGCVVDGCPPGLELTEADIQAELDRRKPGTSRHVTQRREPDTVEILSGVFEGKTTGTPIGLLIR 86 789************************************************************************** PP TIGR00033 78 NkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvklgev 154 N+d+rskdy +i++++RPgHady y++KYg++d++gggrsSaReTa+rvaaGa+a+k+L++ +gi i +++++lg + lcl|FitnessBrowser__PS:Dsui_3204 87 NQDQRSKDYGNIASTFRPGHADYGYTQKYGFRDYRGGGRSSARETAVRVAAGAIARKWLQQRYGISIRGWMSQLGPI 163 ***************************************************************************** PP TIGR00033 155 eleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasall 231 e+++ ++d + +++p+a e+e+++d ++k+ dsvG++++v +++vp g+Gep++d+ldae+a+a++ lcl|FitnessBrowser__PS:Dsui_3204 164 EIPFVD-----AAAIDGNAFFAPNAAIVPELEAYMDALRKSLDSVGAKITVTATGVPPGWGEPVYDRLDAEIAYAMM 235 ***744.....4679************************************************************** PP TIGR00033 232 sinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdle 308 +inAvKgveiG+GF++ ++Gse+ De++ + +n+ GG++GGi++G+di+v++a+Kp+++i++p+++vd++ lcl|FitnessBrowser__PS:Dsui_3204 236 GINAVKGVEIGAGFASIAQKGSEHGDEMT----PAGFLSNHAGGVLGGISTGQDIVVNMAIKPTSSIAQPRRSVDVQ 308 **************************775....678***************************************** PP TIGR00033 309 tkekakatkgRhDpcvvpravpvvEamvalvladallekras 350 ++ at+gRhDpcv +ra+p++Eam+alvl+d++l++ra+ lcl|FitnessBrowser__PS:Dsui_3204 309 GNAVEVATEGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQ 350 **************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (368 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.79 // [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