Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 3609893 Dshi_3275 Chorismate synthase (RefSeq)
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__Dino:3609893 Length = 367 Score = 406 bits (1043), Expect = e-118 Identities = 209/360 (58%), Positives = 256/360 (71%), Gaps = 7/360 (1%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G LFRVTT+GESHG ALG VDG PPG+P+TE LQ LD+R+PG +++TTQRR Sbjct: 1 MSFNTFGHLFRVTTWGESHGPALGATVDGCPPGVPITEEALQVWLDKRKPGQNKFTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD V+ILSGVFEG +TG+ I L+I N DQRS+DY I + FRPGHAD TY QKYG+RDY Sbjct: 61 EPDAVEILSGVFEGQSTGSPIQLMIRNADQRSKDYGDIAEKFRPGHADITYWQKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKF-GIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177 RGGGRSSARETA RVAAG +A+ L + I G +TQMG +D DW Q++QNP Sbjct: 121 RGGGRSSARETAARVAAGGVARAALGALVPDLRITGYMTQMGPHGIDRARFDWEQIDQNP 180 Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237 F+ PD + + L+K G S+GA + V A GVP GLG P++ +LD D+A A+MSI Sbjct: 181 FWTPDAAAAEDWAAYLDGLRKAGSSVGAVIEVTARGVPVGLGAPIYAKLDTDLAAAMMSI 240 Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEITKDG----FQSNHAGGILGGISSGQQIIAHMALK 293 NAVK VEIG+G +L G N DEI G + SNHAGGILGGIS+GQ ++ A+K Sbjct: 241 NAVKAVEIGEGMAAASLTGEANADEIFMGGDGPEYSSNHAGGILGGISTGQDVVVRFAVK 300 Query: 294 PTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNAD 353 PTSSI +TI + G E+ITKGRHDPCVGIRAVP+AEAM+A VL+DHLL R Q D Sbjct: 301 PTSSILTTRQTITKSGAPAEIITKGRHDPCVGIRAVPVAEAMMACVLLDHLLLHRGQVGD 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: 448 Number of extensions: 18 Number of successful extensions: 3 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: 367 Length adjustment: 29 Effective length of query: 332 Effective length of database: 338 Effective search space: 112216 Effective search space used: 112216 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 3609893 Dshi_3275 (Chorismate synthase (RefSeq))
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.21187.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-133 429.5 0.0 5e-133 429.3 0.0 1.0 1 lcl|FitnessBrowser__Dino:3609893 Dshi_3275 Chorismate synthase (R Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3609893 Dshi_3275 Chorismate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.3 0.0 5e-133 5e-133 1 349 [. 10 356 .. 10 358 .. 0.98 Alignments for each domain: == domain 1 score: 429.3 bits; conditional E-value: 5e-133 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiallik 77 +r+tt+GeSHg+alga++dG+P+g+++tee +q l++R+pgq ++t++r+E D+veilsGvfeG+ tG+Pi l+i+ lcl|FitnessBrowser__Dino:3609893 10 FRVTTWGESHGPALGATVDGCPPGVPITEEALQVWLDKRKPGQNKFTTQRREPDAVEILSGVFEGQSTGSPIQLMIR 86 89*************************************************************************** PP TIGR00033 78 NkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLket.agieivayvvklge 153 N d+rskdy di+e++RPgHad ty++KYgi+d++gggrsSaReTaarvaaG va++ L +++i++y++++g lcl|FitnessBrowser__Dino:3609893 87 NADQRSKDYGDIAEKFRPGHADITYWQKYGIRDYRGGGRSSARETAARVAAGGVARAALGALvPDLRITGYMTQMGP 163 *********************************************************99775168************ PP TIGR00033 154 veleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasal 230 +++ ++ e++d++p+ pda a++ +++d ++k+g svG+v+ev +++vpvglG p++ kld+ la+a+ lcl|FitnessBrowser__Dino:3609893 164 HGIDRARFD---WEQIDQNPFWTPDAAAAEDWAAYLDGLRKAGSSVGAVIEVTARGVPVGLGAPIYAKLDTDLAAAM 237 ****98887...59*************************************************************** PP TIGR00033 231 lsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdl 307 +sinAvK+veiG+G +aas +G De+ + d+ + +n+ GGi+GGi++G+d++vr avKp+++i + ++t+++ lcl|FitnessBrowser__Dino:3609893 238 MSINAVKAVEIGEGMAAASLTGEANADEIFMGGDGPEYSSNHAGGILGGISTGQDVVVRFAVKPTSSILTTRQTITK 314 ***************************************************************************** PP TIGR00033 308 etkekakatkgRhDpcvvpravpvvEamvalvladallekra 349 ++ ++ +tkgRhDpcv +ravpv+Eam+a vl+d+ll +r+ lcl|FitnessBrowser__Dino:3609893 315 SGAPAEIITKGRHDPCVGIRAVPVAEAMMACVLLDHLLLHRG 356 *************************************99886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (367 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: 10.57 // [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