Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013644684.1 METBO_RS05465 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000191585.1:WP_013644684.1 Length = 363 Score = 314 bits (804), Expect = 3e-90 Identities = 167/355 (47%), Positives = 231/355 (65%), Gaps = 10/355 (2%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GN+IG++F VTTFG SHG ALG ++DG P G+ L+ D+Q +LD+RRPGTS+ TT R Sbjct: 1 MSGNSIGKIFTVTTFGSSHGTALGAVIDGCPAGLELSTQDIQTELDKRRPGTSKITTSRN 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E DQVK++SG+FEG T GT I L+ N+D S Y IKD RPGH DYT++ +Y + DY Sbjct: 61 EMDQVKLVSGIFEGKTDGTPITALVYNSDMDSSAYENIKDTPRPGHGDYTWKARYDVYDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVE----QN 176 RGGGR S R T V GA+AKK L I++ +TQ+G I D D +++E QN Sbjct: 121 RGGGRGSGRVTIGHVIGGAVAKK-LLNTLNIKVISHVTQVGTIKADPVDVNELETNINQN 179 Query: 177 PFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMS 236 C D + + ++ + KK GDSIG V V PAGLG+P+F +LDA++A LM Sbjct: 180 AVRCADLEAAERMEAEIIETKKSGDSIGGIVETVVLNPPAGLGDPIFGKLDAELAGGLMG 239 Query: 237 INAVKGVEIGDGFDVVALRGSQNRDEITKD----GFQSNHAGGILGGISSGQQIIAHMAL 292 I +VKGVEIG GF L+GSQ DE + ++NH+GGILGGI++G I MA+ Sbjct: 240 IGSVKGVEIGLGFKSAELKGSQMNDEFLIETNTIKTRTNHSGGILGGITTGMPINIRMAV 299 Query: 293 KPTSSITVPGRTIN-RFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLR 346 KPT SI++ +T++ + E +++ +GRHDPC+ R +AEA ++I+L D L+R Sbjct: 300 KPTPSISLTQKTVDTKSMESKDILIQGRHDPCICPRVTTVAEATVSIILADQLIR 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: 355 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: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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 WP_013644684.1 METBO_RS05465 (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.23259.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-141 455.1 3.8 8.1e-141 455.0 3.8 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013644684.1 METBO_RS05465 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013644684.1 METBO_RS05465 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.0 3.8 8.1e-141 8.1e-141 1 347 [. 10 355 .. 10 359 .. 0.98 Alignments for each domain: == domain 1 score: 455.0 bits; conditional E-value: 8.1e-141 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++ttfG+SHg alga+idG+Paglel+++diq+el++Rrpg+s+ t++r+E D+v+++sG+feGkT+G lcl|NCBI__GCF_000191585.1:WP_013644684.1 10 FTVTTFGSSHGTALGAVIDGCPAGLELSTQDIQTELDKRRPGTSKITTSRNEMDQVKLVSGIFEGKTDG 78 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+ l++N d++s+ ye+ik++pRPgH dyt +Y ++d++gggr S+R+T+++v+ GavakklL+ lcl|NCBI__GCF_000191585.1:WP_013644684.1 79 TPITALVYNSDMDSSAYENIKDTPRPGHGDYTWKARYDVYDYRGGGRGSGRVTIGHVIGGAVAKKLLNT 147 *******************************************************************99 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +i+++++v+++g ++++ ++e + +++++ vrc+d ea+++me+ei + kk+gds+Gg+ve+vv lcl|NCBI__GCF_000191585.1:WP_013644684.1 148 -LNIKVISHVTQVGTIKADPVDVNE-LETNINQNAVRCADLEAAERMEAEIIETKKSGDSIGGIVETVV 214 .88****************988887.999**************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 n p+glG+p+f kldaela l++i vKgveiG GF++a+ +Gs++nDe+ +e++ i+++tn+sGGi lcl|NCBI__GCF_000191585.1:WP_013644684.1 215 LNPPAGLGDPIFGKLDAELAGGLMGIGSVKGVEIGLGFKSAELKGSQMNDEFLIETNTIKTRTNHSGGI 283 ********************************************************************* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvladal 344 +GGit+G++i++r+avKp+p+i+ +ktvd++ +e+ + +gRhDpc+ pr++ v+Ea v+++lad+l lcl|NCBI__GCF_000191585.1:WP_013644684.1 284 LGGITTGMPINIRMAVKPTPSISLTQKTVDTKSMESKDILiQGRHDPCICPRVTTVAEATVSIILADQL 352 **************************************999**************************** PP TIGR00033 345 lek 347 ++ lcl|NCBI__GCF_000191585.1:WP_013644684.1 353 IRA 355 986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (363 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: 7.07 // [ok]
This GapMind analysis is from Apr 10 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