Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011384000.1 AMB_RS08025 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000009985.1:WP_011384000.1 Length = 362 Score = 464 bits (1195), Expect = e-135 Identities = 233/358 (65%), Positives = 280/358 (78%), Gaps = 8/358 (2%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GN G LFR TTFGESHG A+GC+VDGVP IPLTEAD+QH LD+R+PG +R+TTQRR Sbjct: 1 MSGNGFGHLFRFTTFGESHGPAIGCVVDGVPARIPLTEADIQHYLDQRKPGQNRFTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD+VKILSGVFEG+TTGTSIGLLIENTDQRS+DY IKD +RPGHAD+ Y+QKYG+RDY Sbjct: 61 EPDEVKILSGVFEGLTTGTSIGLLIENTDQRSKDYGEIKDTYRPGHADWVYQQKYGIRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYL-AEKFGIEIRGCLTQMGDIPLDIK--DWSQVEQNP 177 RGGGRSSARETAMRVAAGAIA+K L A G+ IRG + QMG +D DW+++ NP Sbjct: 121 RGGGRSSARETAMRVAAGAIARKVLDALAPGLSIRGAMVQMGPHAIDRSRWDWAELGNNP 180 Query: 178 FFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSI 237 F+CPD + +E + ++K G SIG V VVASGVP GLG PV+D+LDAD+A A+MSI Sbjct: 181 FWCPDGAAAKSWEEYLDTIRKSGSSIGGVVEVVASGVPVGLGAPVYDKLDADLAKAMMSI 240 Query: 238 NAVKGVEIGDGFDVVALRGSQNRDEIT-----KDGFQSNHAGGILGGISSGQQIIAHMAL 292 NAVKGVEIGDGF AL G +N DE+ + GF SNHAGGILGGIS+GQ ++ +A+ Sbjct: 241 NAVKGVEIGDGFAAAALSGEENADEMRMGNDGQVGFLSNHAGGILGGISTGQDVVVRLAV 300 Query: 293 KPTSSITVPGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQ 350 KPTSSI P ++++ G VE+ TKGRHDPCV IRAVP+AEAM+A L DHLLR AQ Sbjct: 301 KPTSSILTPKQSVDAKGNNVEVSTKGRHDPCVAIRAVPVAEAMMACTLADHLLRSLAQ 358 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: 471 Number of extensions: 13 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: 362 Length adjustment: 29 Effective length of query: 332 Effective length of database: 333 Effective search space: 110556 Effective search space used: 110556 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_011384000.1 AMB_RS08025 (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.18409.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-140 451.6 0.0 9.8e-140 451.4 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011384000.1 AMB_RS08025 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384000.1 AMB_RS08025 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.4 0.0 9.8e-140 9.8e-140 1 349 [. 10 357 .. 10 359 .. 0.98 Alignments for each domain: == domain 1 score: 451.4 bits; conditional E-value: 9.8e-140 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHg+a+g+++dG+Pa ++lte+diq++l++R+pgq r+t++r+E Dev+ilsGvfeG TtG lcl|NCBI__GCF_000009985.1:WP_011384000.1 10 FRFTTFGESHGPAIGCVVDGVPARIPLTEADIQHYLDQRKPGQNRFTTQRREPDEVKILSGVFEGLTTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 + i lli+N+d+rskdy +ik+++RPgHad++y++KYgi+d++gggrsSaReTa+rvaaGa+a+k L+ lcl|NCBI__GCF_000009985.1:WP_011384000.1 79 TSIGLLIENTDQRSKDYGEIKDTYRPGHADWVYQQKYGIRDYRGGGRSSARETAMRVAAGAIARKVLDA 147 *******************************************************************98 PP TIGR00033 139 ta.gieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevv 206 a g+ i + +v++g +++++ + +l ++p+ cpd a+k ee++d+++k+g s+Ggvvevv lcl|NCBI__GCF_000009985.1:WP_011384000.1 148 LApGLSIRGAMVQMGPHAIDRSRWDW---AELGNNPFWCPDGAAAKSWEEYLDTIRKSGSSIGGVVEVV 213 6549****************988884...68899*********************************** PP TIGR00033 207 vsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsG 274 +s+vpvglG p++dklda la+a++sinAvKgveiGdGF+aa G e De+ + d+++ + +n+ G lcl|NCBI__GCF_000009985.1:WP_011384000.1 214 ASGVPVGLGAPVYDKLDADLAKAMMSINAVKGVEIGDGFAAAALSGEENADEMRMGnDGQVGFLSNHAG 282 ******************************************************998999********* PP TIGR00033 275 GieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvlada 343 Gi+GGi++G+d++vr avKp+++i +p+++vd ++++ tkgRhDpcv++ravpv+Eam+a +lad+ lcl|NCBI__GCF_000009985.1:WP_011384000.1 283 GILGGISTGQDVVVRLAVKPTSSILTPKQSVDAKGNNVEVSTKGRHDPCVAIRAVPVAEAMMACTLADH 351 **********************************99999999*************************** PP TIGR00033 344 llekra 349 ll++ a lcl|NCBI__GCF_000009985.1:WP_011384000.1 352 LLRSLA 357 **9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (362 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: 7.76 // [ok]
This GapMind analysis is from Apr 09 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