Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013451463.1 CALNI_RS06775 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000183405.1:WP_013451463.1 Length = 351 Score = 387 bits (995), Expect = e-112 Identities = 195/347 (56%), Positives = 260/347 (74%), Gaps = 5/347 (1%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGN+ G++FR+TTFGESHG A+G ++DGVP IP++E ++Q +LDRR+PG S TT R Sbjct: 1 MAGNSFGRIFRITTFGESHGKAVGVVLDGVPSKIPISEDEIQRELDRRKPGQSELTTPRS 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVF+G+TTGT I +++ N +Q+S+DY A+K++FRPGHADYTY+ KYG+RDY Sbjct: 61 EDDKVEILSGVFDGMTTGTPICMVVYNKNQKSKDYDAVKNLFRPGHADYTYQMKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLD--IKDWSQVEQNPF 178 RGGGRSS+RET RV AGAIAKK L +K+ IEI G + Q+G + + +KD+ +E NP Sbjct: 121 RGGGRSSSRETIGRVCAGAIAKKIL-KKYNIEIFGYVKQVGYVKGEKLVKDF--IENNPV 177 Query: 179 FCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSIN 238 DP+K +L+ +K GDS+GA V ++ SGVP GLGEPVFDRL+A+I A++SI Sbjct: 178 RMGDPEKYKEAYDLILDVKSRGDSVGALVEIIVSGVPVGLGEPVFDRLNAEIGKAILSIP 237 Query: 239 AVKGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSI 298 AVKG+E G GF VV GS N DEIT GF +N+AGG LGGISSGQ I+ A+KP SSI Sbjct: 238 AVKGIEFGAGFSVVEHFGSINNDEITPYGFMTNNAGGTLGGISSGQDIVFRFAVKPPSSI 297 Query: 299 TVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLL 345 + TI+ G +++T+GRHDPCV R VPIAEAM +IV++D ++ Sbjct: 298 LIEKNTIDIMGNPKKIVTEGRHDPCVAPRVVPIAEAMTSIVIVDFMM 344 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: 399 Number of extensions: 18 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: 351 Length adjustment: 29 Effective length of query: 332 Effective length of database: 322 Effective search space: 106904 Effective search space used: 106904 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_013451463.1 CALNI_RS06775 (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.23265.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-137 441.6 0.6 1.1e-136 441.4 0.6 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013451463.1 CALNI_RS06775 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013451463.1 CALNI_RS06775 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.4 0.6 1.1e-136 1.1e-136 1 347 [. 10 346 .. 10 350 .. 0.98 Alignments for each domain: == domain 1 score: 441.4 bits; conditional E-value: 1.1e-136 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHgka+g+++dG+P+ ++++e++iq+el+rR+pgqs+lt++r+E+D+veilsGvf G TtG lcl|NCBI__GCF_000183405.1:WP_013451463.1 10 FRITTFGESHGKAVGVVLDGVPSKIPISEDEIQRELDRRKPGQSELTTPRSEDDKVEILSGVFDGMTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+++++Nk+++skdy+ +k+l+RPgHadyty+ KYgi+d++gggrsS+ReT++rv aGa+akk Lk+ lcl|NCBI__GCF_000183405.1:WP_013451463.1 79 TPICMVVYNKNQKSKDYDAVKNLFRPGHADYTYQMKYGIRDYRGGGRSSSRETIGRVCAGAIAKKILKK 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ++iei +yv ++g v+ e+ k+ ++++pvr+ d+e+ ke ++i +k+ gdsvG+ ve++v lcl|NCBI__GCF_000183405.1:WP_013451463.1 148 -YNIEIFGYVKQVGYVKGEK-----LVKDFIENNPVRMGDPEKYKEAYDLILDVKSRGDSVGALVEIIV 210 .99**************995.....456689************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 s+vpvglGep+fd+l+ae+++a+lsi+AvKg+e+G+GF+ ++ Gs nDe+ + + + tnn GG+ lcl|NCBI__GCF_000183405.1:WP_013451463.1 211 SGVPVGLGEPVFDRLNAEIGKAILSIPAVKGIEFGAGFSVVEHFGSINNDEI----TPYGFMTNNAGGT 275 **************************************************77....6899********* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GGi+ G+di++r avKp ++i +++t+d+ +++k +t+gRhDpcv+pr+vp++Eam+++v++d ++ lcl|NCBI__GCF_000183405.1:WP_013451463.1 276 LGGISSGQDIVFRFAVKPPSSILIEKNTIDIMGNPKKIVTEGRHDPCVAPRVVPIAEAMTSIVIVDFMM 344 ******************************************************************987 PP TIGR00033 346 ek 347 + lcl|NCBI__GCF_000183405.1:WP_013451463.1 345 IN 346 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (351 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: 9.46 // [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