Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_028319913.1 H567_RS0100685 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000422285.1:WP_028319913.1 Length = 366 Score = 353 bits (906), Expect = e-102 Identities = 181/350 (51%), Positives = 230/350 (65%), Gaps = 1/350 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M GNT GQ R+TTFGESHG A+G +VDG PPG+ L+E D + RRRPGT + + R Sbjct: 1 MPGNTFGQALRITTFGESHGPAVGAVVDGCPPGLALSETDFLEAMARRRPGTRPFDSPRS 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E DQV +LSGVFE TTGT I LLI N D S+ Y ++ +FRPGHAD +Y KYG RD+ Sbjct: 61 EKDQVILLSGVFEDRTTGTPITLLIHNQDADSRPYEQLRHIFRPGHADISYHMKYGHRDH 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGR+SARETA RVAAG IA K L G+ ++G ++ + D NPF C Sbjct: 121 RGGGRASARETAARVAAGVIAGKIL-HPAGVSVQGYTVELAGVQAGKGDIQNAAGNPFRC 179 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 DP+ + E + A++ GDS G + V+ +G P GLGEPVFD+LDAD+A A+MS+ AV Sbjct: 180 ADPEAAARMAEALEAIRATGDSAGGIIEVLITGCPPGLGEPVFDKLDADLAKAVMSVGAV 239 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIG GF+ LRGS+N D I + F SNHAGGILGG+S+G I+ A+KP SI + Sbjct: 240 KGVEIGAGFESARLRGSENNDPIMPEAFASNHAGGILGGVSTGADIVLRAAVKPIPSIGM 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350 +TI+R G+ + GRHD R VP+ EAM+ +VL DH LR RAQ Sbjct: 300 EQQTIDRNGKPFRLKLSGRHDTTAVSRIVPVLEAMVLLVLADHYLRARAQ 349 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: 409 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: 366 Length adjustment: 29 Effective length of query: 332 Effective length of database: 337 Effective search space: 111884 Effective search space used: 111884 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_028319913.1 H567_RS0100685 (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.11134.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-127 411.1 0.1 2e-127 410.9 0.1 1.0 1 lcl|NCBI__GCF_000422285.1:WP_028319913.1 H567_RS0100685 chorismate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000422285.1:WP_028319913.1 H567_RS0100685 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 410.9 0.1 2e-127 2e-127 1 349 [. 10 348 .. 10 350 .. 0.97 Alignments for each domain: == domain 1 score: 410.9 bits; conditional E-value: 2e-127 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 lr+ttfGeSHg+a+ga++dG+P+gl l+e d+ ++++rRrpg+ + ++r+E+D+v +lsGvfe +TtG lcl|NCBI__GCF_000422285.1:WP_028319913.1 10 LRITTFGESHGPAVGAVVDGCPPGLALSETDFLEAMARRRPGTRPFDSPRSEKDQVILLSGVFEDRTTG 78 699****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi+lli+N+d +s++ye++++++RPgHad y KYg +d++gggr+SaReTaarvaaG++a k L+ lcl|NCBI__GCF_000422285.1:WP_028319913.1 79 TPITLLIHNQDADSRPYEQLRHIFRPGHADISYHMKYGHRDHRGGGRASARETAARVAAGVIAGKILHP 147 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ag+ + +y+v+l+ v++ + ++ +++ +p+rc+d+ea+++m e ++ ++ gds Gg++ev++ lcl|NCBI__GCF_000422285.1:WP_028319913.1 148 -AGVSVQGYTVELAGVQAGKGDIQ-----NAAGNPFRCADPEAAARMAEALEAIRATGDSAGGIIEVLI 210 .99*************99974444.....57779*********************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++ p glGep+fdklda la+a++s+ AvKgveiG+GFe+a+ rGse nD+++ e + +n+ GGi lcl|NCBI__GCF_000422285.1:WP_028319913.1 211 TGCPPGLGEPVFDKLDADLAKAVMSVGAVKGVEIGAGFESARLRGSENNDPIMPE----AFASNHAGGI 275 ***************************************************9876....699******* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladall 345 +GG+++G di++r+avKpip+i+ +++t+d ++k+ gRhD ++v r+vpv Eamv lvlad++l lcl|NCBI__GCF_000422285.1:WP_028319913.1 276 LGGVSTGADIVLRAAVKPIPSIGMEQQTIDRNGKPFRLKLSGRHDTTAVSRIVPVLEAMVLLVLADHYL 344 *******************************999999999***************************** PP TIGR00033 346 ekra 349 + ra lcl|NCBI__GCF_000422285.1:WP_028319913.1 345 RARA 348 9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (366 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: 9.29 // [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