Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate RR42_RS06485 RR42_RS06485 chorismate synthase
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__Cup4G11:RR42_RS06485 Length = 372 Score = 478 bits (1230), Expect = e-139 Identities = 231/360 (64%), Positives = 290/360 (80%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT+G LF VTTFGESHG A+G +VDG PPG+ LTEAD+Q DLDRR+PGTSR+ TQR+ Sbjct: 1 MSGNTLGLLFTVTTFGESHGPAIGAVVDGCPPGMSLTEADIQLDLDRRKPGTSRHVTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPDQV+ILSGVFEG TTGT I LLI NTDQRS+DY I + FRPGHADYTY QKYG+RDY Sbjct: 61 EPDQVEILSGVFEGKTTGTPICLLIRNTDQRSKDYGNIVETFRPGHADYTYWQKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSAR TA VAA A+A+K+L E++G EIRG ++Q+G++ + DW++V +NPFF Sbjct: 121 RGGGRSSARLTAPVVAAAAVARKWLREQYGTEIRGYMSQLGEVRVPFVDWAEVPENPFFA 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 P+ + + L+ M AL+++GDS+GA++ VVAS VP GLGEP+FD+LDADIAHA+M INAV Sbjct: 181 PNAEIVPELETYMDALRRDGDSVGARIEVVASHVPVGLGEPLFDKLDADIAHAMMGINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF+ V+ RGS + D ++ +GF+ N+AGG+LGGIS+GQ + +A+KPTSSI Sbjct: 241 KGVEIGAGFESVSQRGSVHGDSLSAEGFRGNNAGGVLGGISTGQDVTVSLAIKPTSSIRT 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360 P +I++ G+ + T GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQ DVK D PR Sbjct: 301 PRESIDKAGQPATVETFGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQCGDVKVDTPR 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: 466 Number of extensions: 15 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: 372 Length adjustment: 30 Effective length of query: 331 Effective length of database: 342 Effective search space: 113202 Effective search space used: 113202 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 RR42_RS06485 RR42_RS06485 (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.26500.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-143 463.9 0.0 1.8e-143 463.7 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS06485 RR42_RS06485 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS06485 RR42_RS06485 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.7 0.0 1.8e-143 1.8e-143 1 350 [. 10 350 .. 10 351 .. 0.98 Alignments for each domain: == domain 1 score: 463.7 bits; conditional E-value: 1.8e-143 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++ttfGeSHg+a+ga++dG+P+g++lte+diq +l+rR+pg+sr+ ++r+E D+veilsGvfeGkTtG lcl|FitnessBrowser__Cup4G11:RR42_RS06485 10 FTVTTFGESHGPAIGAVVDGCPPGMSLTEADIQLDLDRRKPGTSRHVTQRQEPDQVEILSGVFEGKTTG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+lli+N+d+rskdy +i e++RPgHadyty++KYgi+d++gggrsSaR Ta vaa ava+k+L+e lcl|FitnessBrowser__Cup4G11:RR42_RS06485 79 TPICLLIRNTDQRSKDYGNIVETFRPGHADYTYWQKYGIRDYRGGGRSSARLTAPVVAAAAVARKWLRE 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ++g+ei +y+++lgev++++ ++ ++p+++p+ae e+e ++d +++dgdsvG+++evv+ lcl|FitnessBrowser__Cup4G11:RR42_RS06485 148 QYGTEIRGYMSQLGEVRVPFVDWA-----EVPENPFFAPNAEIVPELETYMDALRRDGDSVGARIEVVA 211 *******************85555.....5889************************************ PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 s vpvglGeplfdklda +a+a+++inAvKgveiG+GFe++s+rGs + D l +e ++ nn GG+ lcl|FitnessBrowser__Cup4G11:RR42_RS06485 212 SHVPVGLGEPLFDKLDADIAHAMMGINAVKGVEIGAGFESVSQRGSVHGDSLSAE----GFRGNNAGGV 276 **************************************************87766....689******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi++G+d++v+ a+Kp+++i++p++++d+++++++ t gRhDpcv +ra+p++Eam+alvl+d++l lcl|FitnessBrowser__Cup4G11:RR42_RS06485 277 LGGISTGQDVTVSLAIKPTSSIRTPRESIDKAGQPATVETFGRHDPCVGIRATPIAEAMLALVLMDHAL 345 ********************************************************************* PP TIGR00033 346 ekras 350 ++ra+ lcl|FitnessBrowser__Cup4G11:RR42_RS06485 346 RHRAQ 350 *9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (372 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: 8.15 // [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