Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011424282.1 RHE_RS04715 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000092045.1:WP_011424282.1 Length = 365 Score = 398 bits (1022), Expect = e-115 Identities = 211/368 (57%), Positives = 259/368 (70%), Gaps = 16/368 (4%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G LFRVTT+GESHG ALGC+VDG PPG+ DLQ LD+R+PG SR+ TQRR Sbjct: 1 MSHNTFGHLFRVTTWGESHGPALGCVVDGCPPGLRFKLEDLQVWLDKRKPGQSRFVTQRR 60 Query: 61 EPDQVKILSGVF---EGVT---TGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114 E D VK+LSGV +G T TGT I +LIENTDQRS+DY I +RPGHADYTY+ K Sbjct: 61 EDDLVKVLSGVMLDADGETMTSTGTPISMLIENTDQRSKDYGEIARQYRPGHADYTYDLK 120 Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172 YG+RDYRGGGRSSARETA RVAAG IA+ + G+ +RG L Q+G +D + DW Q Sbjct: 121 YGIRDYRGGGRSSARETAARVAAGGIARLVVP---GVTVRGALVQIGKHKIDRRNWDWDQ 177 Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232 V+QNPFF PD + +E + ++K G SIGA + V+A GVPAGLG P++ +LD DIA Sbjct: 178 VDQNPFFSPDAAIVPVWEEYLDGIRKAGSSIGAVIEVIAEGVPAGLGAPIYSKLDQDIAS 237 Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRD--EITKDG---FQSNHAGGILGGISSGQQII 287 LMSINAVKGVEIG+GF G N D + DG F SN+AGGILGGIS+GQ ++ Sbjct: 238 LLMSINAVKGVEIGNGFAAAETSGEDNADAMRMGNDGTPIFLSNNAGGILGGISTGQPVV 297 Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347 A A+KPTSSI ++I+ G+ V++ TKGRHDPCVGIRAVPI EAM+A + DH LR Sbjct: 298 ARFAVKPTSSILTERQSIDADGKNVDVRTKGRHDPCVGIRAVPIGEAMVACAIADHYLRD 357 Query: 348 RAQNADVK 355 R Q +K Sbjct: 358 RGQTGRLK 365 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: 17 Number of successful extensions: 6 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: 365 Length adjustment: 29 Effective length of query: 332 Effective length of database: 336 Effective search space: 111552 Effective search space used: 111552 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_011424282.1 RHE_RS04715 (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.29003.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-124 401.8 0.0 1.4e-124 401.6 0.0 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011424282.1 RHE_RS04715 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011424282.1 RHE_RS04715 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.6 0.0 1.4e-124 1.4e-124 1 350 [. 10 360 .. 10 361 .. 0.96 Alignments for each domain: == domain 1 score: 401.6 bits; conditional E-value: 1.4e-124 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf...eGk 66 +r+tt+GeSHg+alg+++dG+P+gl+ + ed+q l++R+pgqsr+ ++r+E+D v++lsGv+ G+ lcl|NCBI__GCF_000092045.1:WP_011424282.1 10 FRVTTWGESHGPALGCVVDGCPPGLRFKLEDLQVWLDKRKPGQSRFVTQRREDDLVKVLSGVMldaDGE 78 89************************************************************6444798 PP TIGR00033 67 T...tGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGava 132 T tG+Pi++li+N+d+rskdy +i++++RPgHadyty KYgi+d++gggrsSaReTaarvaaG +a lcl|NCBI__GCF_000092045.1:WP_011424282.1 79 TmtsTGTPISMLIENTDQRSKDYGEIARQYRPGHADYTYDLKYGIRDYRGGGRSSARETAARVAAGGIA 147 85556**************************************************************** PP TIGR00033 133 kklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGg 201 + + g+ + + +v++g+ ++++++ + +++d++p++ pda ee++d ++k+g s+G+ lcl|NCBI__GCF_000092045.1:WP_011424282.1 148 RLVVP---GVTVRGALVQIGKHKIDRRNWDW---DQVDQNPFFSPDAAIVPVWEEYLDGIRKAGSSIGA 210 96655...599**************988884...79********************************* PP TIGR00033 202 vvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrk 269 v+ev++++vp+glG p+++kld +as+l+sinAvKgveiG+GF+aa++ G + D + + d+ + lcl|NCBI__GCF_000092045.1:WP_011424282.1 211 VIEVIAEGVPAGLGAPIYSKLDQDIASLLMSINAVKGVEIGNGFAAAETSGEDNADAMRMGnDGTPIFL 279 ************************************************************9788889** PP TIGR00033 270 tnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamval 338 +nn GGi+GGi++G++++ r avKp+++i ++++++d ++k+ +tkgRhDpcv +ravp+ Eamva lcl|NCBI__GCF_000092045.1:WP_011424282.1 280 SNNAGGILGGISTGQPVVARFAVKPTSSILTERQSIDADGKNVDVRTKGRHDPCVGIRAVPIGEAMVAC 348 ********************************************************************* PP TIGR00033 339 vladallekras 350 +ad++l++r++ lcl|NCBI__GCF_000092045.1:WP_011424282.1 349 AIADHYLRDRGQ 360 *******98875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (365 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: 7.40 // [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