Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate AZOBR_RS10730 AZOBR_RS10730 chorismate synthase
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__azobra:AZOBR_RS10730 Length = 358 Score = 447 bits (1149), Expect = e-130 Identities = 223/356 (62%), Positives = 277/356 (77%), Gaps = 9/356 (2%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGN+ G LFR TT+GESHG A+G +VDG P + LTEAD+Q LD+RRPG SRYTTQR+ Sbjct: 1 MAGNSFGTLFRFTTWGESHGPAIGVVVDGCPSLLSLTEADIQPWLDKRRPGQSRYTTQRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPDQV+ILSGVFEG TTGT + L+IENTDQRS+DYS I FRPGHADYTY +KYG+RDY Sbjct: 61 EPDQVRILSGVFEGRTTGTPVSLMIENTDQRSKDYSEIASKFRPGHADYTYWKKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNPF 178 RGGGRSSARETA RVAAGA+A+K L + G+ +RG L Q+G +D DW++V+ NPF Sbjct: 121 RGGGRSSARETACRVAAGAVARKVLGD--GVTVRGALVQIGPHKVDRSRWDWAEVDNNPF 178 Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238 FCPDP + + ++K G SIGA V VVASG+PAGLG+P++D+LD D+AHA+M+IN Sbjct: 179 FCPDPQAAAEWADYLDGIRKSGSSIGAVVEVVASGLPAGLGDPLYDKLDGDLAHAMMTIN 238 Query: 239 AVKGVEIGDGFDVVALRGSQNRDEIT--KDG---FQSNHAGGILGGISSGQQIIAHMALK 293 AVKGVEIG+GF+ L G QN DE+ DG F+SN AGGILGGIS+GQ ++ A+K Sbjct: 239 AVKGVEIGNGFEAATLTGEQNADEMRAGPDGEPEFRSNLAGGILGGISTGQDVVVRFAVK 298 Query: 294 PTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRA 349 PTSSI P +T++ G++ +++TKGRHDPCVGIRAVP+ EAM+A VL DHLLR RA Sbjct: 299 PTSSILTPRQTVDLQGKDTDILTKGRHDPCVGIRAVPVGEAMMACVLADHLLRHRA 354 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: 461 Number of extensions: 21 Number of successful extensions: 4 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: 358 Length adjustment: 29 Effective length of query: 332 Effective length of database: 329 Effective search space: 109228 Effective search space used: 109228 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 AZOBR_RS10730 AZOBR_RS10730 (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.14207.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-143 461.7 0.0 8.3e-143 461.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS10730 AZOBR_RS10730 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS10730 AZOBR_RS10730 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.5 0.0 8.3e-143 8.3e-143 1 349 [. 10 354 .. 10 356 .. 0.99 Alignments for each domain: == domain 1 score: 461.5 bits; conditional E-value: 8.3e-143 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHg+a+g+++dG+P+ l+lte+diq+ l++Rrpgqsr+t++r+E D+v+ilsGvfeG+TtG lcl|FitnessBrowser__azobra:AZOBR_RS10730 10 FRFTTWGESHGPAIGVVVDGCPSLLSLTEADIQPWLDKRRPGQSRYTTQRQEPDQVRILSGVFEGRTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +P++l+i+N+d+rskdy++i++++RPgHadyty+kKYgi+d++gggrsSaReTa+rvaaGava+k L + lcl|FitnessBrowser__azobra:AZOBR_RS10730 79 TPVSLMIENTDQRSKDYSEIASKFRPGHADYTYWKKYGIRDYRGGGRSSARETACRVAAGAVARKVLGD 147 *******************************************************************99 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 g+ + + +v++g +++++ + ++d++p++cpd++a++e +++d ++k+g s+G+vvevv+ lcl|FitnessBrowser__azobra:AZOBR_RS10730 148 --GVTVRGALVQIGPHKVDRSRWD---WAEVDNNPFFCPDPQAAAEWADYLDGIRKSGSSIGAVVEVVA 211 ..9****************98887...479*************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275 s++p+glG+pl+dkld+ la+a+++inAvKgveiG+GFeaa+ +G + De+ + d++ ++++n GG lcl|FitnessBrowser__azobra:AZOBR_RS10730 212 SGLPAGLGDPLYDKLDGDLAHAMMTINAVKGVEIGNGFEAATLTGEQNADEMRAGpDGEPEFRSNLAGG 280 ******************************************************99999********** PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344 i+GGi++G+d++vr avKp+++i +p++tvdl++k++ tkgRhDpcv +ravpv Eam+a vlad+l lcl|FitnessBrowser__azobra:AZOBR_RS10730 281 ILGGISTGQDVVVRFAVKPTSSILTPRQTVDLQGKDTDILTKGRHDPCVGIRAVPVGEAMMACVLADHL 349 ********************************************************************* PP TIGR00033 345 lekra 349 l++ra lcl|FitnessBrowser__azobra:AZOBR_RS10730 350 LRHRA 354 **986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (358 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: 10.24 // [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