Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_026608243.1 METAC_RS0119090 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000427445.1:WP_026608243.1 Length = 367 Score = 425 bits (1093), Expect = e-124 Identities = 217/363 (59%), Positives = 265/363 (73%), Gaps = 16/363 (4%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+ NT G LFRVTTFGESHG A+GC+VDG PP + L EAD+QH LD+RRPGTSR+TTQR+ Sbjct: 1 MSHNTFGHLFRVTTFGESHGPAIGCVVDGCPPLLELEEADIQHFLDQRRPGTSRFTTQRQ 60 Query: 61 EPDQVKILSGVF------EGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQK 114 E DQVKILSGVF VTTGT I L+IENTDQRS+DY IKD +RPGHAD+ Y+ K Sbjct: 61 EADQVKILSGVFVDDKTGRQVTTGTPIALMIENTDQRSKDYDDIKDKYRPGHADFAYDLK 120 Query: 115 YGLRDYRGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIK--DWSQ 172 YG+RD RGGGRSSARETA RVAAGA+A+K +A G+ +RG L Q+G +D DW++ Sbjct: 121 YGIRDPRGGGRSSARETASRVAAGAVARKVIA---GVRVRGALVQIGPHKIDRARWDWAE 177 Query: 173 VEQNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAH 232 ++NPFFCPD + + + ++K G SIGA + +VA VP G G P++ +LDA++A Sbjct: 178 TQKNPFFCPDAEAAAFFETYLDEIRKAGSSIGAVIEIVAENVPVGWGAPIYGKLDAELAG 237 Query: 233 ALMSINAVKGVEIGDGFDVVALRGSQNRDEITKDG-----FQSNHAGGILGGISSGQQII 287 ALMSINAVKGVEIGDGF L G N DE+ F SNHAGG+LGGIS+GQ ++ Sbjct: 238 ALMSINAVKGVEIGDGFAAAELSGEANADEMRAGNEGAPRFLSNHAGGVLGGISTGQPLV 297 Query: 288 AHMALKPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347 A A+KPTSSI P TI+R G E E++TKGRHDPCVGIRAVP+ EAM+A VL D LR Sbjct: 298 ARFAVKPTSSILQPRLTIDRGGAETEIVTKGRHDPCVGIRAVPVGEAMVACVLADQFLRH 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: 442 Number of extensions: 22 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: 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 WP_026608243.1 METAC_RS0119090 (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.20811.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-135 435.3 0.0 9e-135 435.1 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026608243.1 METAC_RS0119090 chorismate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026608243.1 METAC_RS0119090 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.1 0.0 9e-135 9e-135 1 349 [. 10 359 .. 10 361 .. 0.96 Alignments for each domain: == domain 1 score: 435.1 bits; conditional E-value: 9e-135 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvf....eG 65 +r+ttfGeSHg+a+g+++dG+P+ lel+e+diq+ l++Rrpg+sr+t++r+E+D+v+ilsGvf +G lcl|NCBI__GCF_000427445.1:WP_026608243.1 10 FRVTTFGESHGPAIGCVVDGCPPLLELEEADIQHFLDQRRPGTSRFTTQRQEADQVKILSGVFvddkTG 78 89************************************************************8444434 PP TIGR00033 66 ..kTtGaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGava 132 TtG+Pial+i+N+d+rskdy+dik+++RPgHad++y KYgi+d +gggrsSaReTa rvaaGava lcl|NCBI__GCF_000427445.1:WP_026608243.1 79 rqVTTGTPIALMIENTDQRSKDYDDIKDKYRPGHADFAYDLKYGIRDPRGGGRSSARETASRVAAGAVA 147 3369***************************************************************** PP TIGR00033 133 kklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGg 201 +k ++ +++ + +v++g ++++ + +++k+p++cpdaea++ e ++d+++k+g s+G+ lcl|NCBI__GCF_000427445.1:WP_026608243.1 148 RKVIAG---VRVRGALVQIGPHKIDRARWDW---AETQKNPFFCPDAEAAAFFETYLDEIRKAGSSIGA 210 ***987...99**************987774...67888****************************** PP TIGR00033 202 vvevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrk 269 v+e+v++nvpvg+G p++ kldaela al+sinAvKgveiGdGF+aa+ G De+ + ++ r+ lcl|NCBI__GCF_000427445.1:WP_026608243.1 211 VIEIVAENVPVGWGAPIYGKLDAELAGALMSINAVKGVEIGDGFAAAELSGEANADEMRAGnEGAPRFL 279 ***********************************************************9978889*** PP TIGR00033 270 tnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamval 338 +n+ GG++GGi++G++++ r avKp+++i +p+ t+d + e+ +tkgRhDpcv +ravpv Eamva lcl|NCBI__GCF_000427445.1:WP_026608243.1 280 SNHAGGVLGGISTGQPLVARFAVKPTSSILQPRLTIDRGGAETEIVTKGRHDPCVGIRAVPVGEAMVAC 348 ********************************************************************* PP TIGR00033 339 vladallekra 349 vlad++l++r+ lcl|NCBI__GCF_000427445.1:WP_026608243.1 349 VLADQFLRHRG 359 ********987 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: 7.66 // [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