Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate CCNA_03256 CCNA_03256 chorismate synthase
Query= SwissProt::P12008 (361 letters) >FitnessBrowser__Caulo:CCNA_03256 Length = 372 Score = 415 bits (1067), Expect = e-121 Identities = 218/363 (60%), Positives = 259/363 (71%), Gaps = 16/363 (4%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G LFRVTT+GESHG ALGC+VDG PPGI LT +Q LD+RRPG ++ TQR+ Sbjct: 1 MSHNTFGHLFRVTTWGESHGPALGCVVDGCPPGIALTAEMIQVFLDKRRPGNGKFVTQRQ 60 Query: 61 EPDQVKILSGVFEGV------TTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114 EPD V+ILSGVFE TTGT I L+IENTDQRS+DYS I FRPGHADY Y K Sbjct: 61 EPDAVRILSGVFEDARSNGQRTTGTPISLMIENTDQRSKDYSEIAQAFRPGHADYAYFAK 120 Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172 YG+RDYRGGGRSSARETA RVAAGA+A+ + G+ +R L Q+G +D DW+Q Sbjct: 121 YGVRDYRGGGRSSARETAARVAAGAVARLIIP---GVTVRAALVQIGPHKIDRSNWDWAQ 177 Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232 EQNP++ PD + +E + ++K G S GA V V A+GVPAG G P++ +LDA++A Sbjct: 178 TEQNPYWSPDAAIVPVWEEHLEKIRKAGSSTGAVVEVEATGVPAGWGAPLYAKLDAELAA 237 Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEITK--DG---FQSNHAGGILGGISSGQQII 287 ALMSINA KGVEIGDGFD AL G N D + DG FQSNHAGGILGGISSGQ I+ Sbjct: 238 ALMSINAAKGVEIGDGFDSAALTGEDNADTMRMGDDGQPVFQSNHAGGILGGISSGQPIV 297 Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347 A +A KPTSSI +P T+N GEE+E+ TKGRHDPCVGIR VP+ EAM A VL D LR Sbjct: 298 ARVAFKPTSSILIPRETVNEAGEEIELRTKGRHDPCVGIRGVPVVEAMTACVLADAFLRH 357 Query: 348 RAQ 350 R Q Sbjct: 358 RGQ 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: 415 Number of extensions: 13 Number of successful extensions: 5 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 CCNA_03256 CCNA_03256 (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.19499.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-130 421.5 0.0 1.3e-130 421.3 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03256 CCNA_03256 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03256 CCNA_03256 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 421.3 0.0 1.3e-130 1.3e-130 1 350 [. 10 360 .. 10 361 .. 0.96 Alignments for each domain: == domain 1 score: 421.3 bits; conditional E-value: 1.3e-130 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfe.....G.kT 67 +r+tt+GeSHg+alg+++dG+P+g+ lt+e+iq l++Rrpg++++ ++r+E D+v+ilsGvfe G +T lcl|FitnessBrowser__Caulo:CCNA_03256 10 FRVTTWGESHGPALGCVVDGCPPGIALTAEMIQVFLDKRRPGNGKFVTQRQEPDAVRILSGVFEdarsnGqRT 82 89************************************************************9744444446* PP TIGR00033 68 tGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketa 140 tG+Pi+l+i+N+d+rskdy++i++ +RPgHady+y+ KYg++d++gggrsSaReTaarvaaGava+ + lcl|FitnessBrowser__Caulo:CCNA_03256 83 TGTPISLMIENTDQRSKDYSEIAQAFRPGHADYAYFAKYGVRDYRGGGRSSARETAARVAAGAVARLIIPG-- 153 *****************************************************************977655.. PP TIGR00033 141 gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvg 213 + + a +v++g ++++++ + +++++p pda ee ++k++k+g s G+vvev +++vp+g lcl|FitnessBrowser__Caulo:CCNA_03256 154 -VTVRAALVQIGPHKIDRSNWDW---AQTEQNPYWSPDAAIVPVWEEHLEKIRKAGSSTGAVVEVEATGVPAG 222 .99**************998884...68899****************************************** PP TIGR00033 214 lGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGGieGGitnGed 285 +G pl+ kldaela+al+sinA+KgveiGdGF++a +G + D + + d++ +++n+ GGi+GGi+ G++ lcl|FitnessBrowser__Caulo:CCNA_03256 223 WGAPLYAKLDAELAAALMSINAAKGVEIGDGFDSAALTGEDNADTMRMGdDGQPVFQSNHAGGILGGISSGQP 295 ***********************************************99677889****************** PP TIGR00033 286 irvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladallekras 350 i+ r+a+Kp+++i p++tv+ +++e +tkgRhDpcv +r vpvvEam+a vlada+l++r++ lcl|FitnessBrowser__Caulo:CCNA_03256 296 IVARVAFKPTSSILIPRETVNEAGEEIELRTKGRHDPCVGIRGVPVVEAMTACVLADAFLRHRGQ 360 *************************************************************9976 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: 9.60 // [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