Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate 206322 DVU0894 chorismate synthase
Query= SwissProt::P12008 (361 letters) >MicrobesOnline__882:206322 Length = 354 Score = 386 bits (991), Expect = e-112 Identities = 191/348 (54%), Positives = 252/348 (72%), Gaps = 1/348 (0%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GNT+G+LFR+TT+GESHG LG ++DG P GI L EA +Q +LD RRPG + +T R+ Sbjct: 1 MSGNTLGRLFRLTTYGESHGAGLGGVIDGCPAGIALDEAVIQRELDLRRPGGNSASTTRQ 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD+V++LSGVFEGVTTGT I +EN DQRS+DY I ++RPGHAD+TY+ K+G+RDY Sbjct: 61 EPDRVRLLSGVFEGVTTGTPIAFHVENVDQRSRDYGEIARLYRPGHADFTYDAKFGVRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGR+S RET RVA GAIA+ LA + GI +R ++G +P D+ D + +Q PFF Sbjct: 121 RGGGRASGRETLSRVAGGAIAQALLA-RHGIAVRAFTVELGGVPADLVDVAGAQQRPFFS 179 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDPD ++A ++++R +K EGD++G V V A+GVPAGLGEPVFD+LDA +A+ALMS+ AV Sbjct: 180 PDPDVVEAWEDMVRTVKGEGDTLGGIVQVEATGVPAGLGEPVFDKLDAVLAYALMSVGAV 239 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVE+G GF+ + GS N D I GF +NHAGGILGGIS+G+ I+ A+KP SI Sbjct: 240 KGVEVGAGFEAARMHGSDNNDPIVPSGFFTNHAGGILGGISNGETIVLRAAVKPIPSIAQ 299 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQR 348 TI+R G+ + GRHD R VP+ +AM A+VL D LL QR Sbjct: 300 EQITIDRDGKPSALFIAGRHDISAIPRIVPVLKAMTALVLADMLLMQR 347 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: 397 Number of extensions: 18 Number of successful extensions: 2 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: 354 Length adjustment: 29 Effective length of query: 332 Effective length of database: 325 Effective search space: 107900 Effective search space used: 107900 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 206322 DVU0894 (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.23012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-128 412.4 0.1 8e-128 412.2 0.1 1.0 1 lcl|MicrobesOnline__882:206322 DVU0894 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206322 DVU0894 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.2 0.1 8e-128 8e-128 1 348 [. 10 347 .. 10 350 .. 0.97 Alignments for each domain: == domain 1 score: 412.2 bits; conditional E-value: 8e-128 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGaPiallikNk 79 +rltt+GeSHg+ lg +idG+Pag+ l+e+ iq+el+ Rrpg +++r+E D+v++lsGvfeG TtG+Pia+ ++N lcl|MicrobesOnline__882:206322 10 FRLTTYGESHGAGLGGVIDGCPAGIALDEAVIQRELDLRRPGGNSASTTRQEPDRVRLLSGVFEGVTTGTPIAFHVENV 88 89***************************************************************************** PP TIGR00033 80 dvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLketagieivayvvklgevelee 158 d+rs+dy +i++l+RPgHad+ty K+g++d++gggr+S+ReT rva Ga+a++lL++ +gi + a++v+lg v ++ lcl|MicrobesOnline__882:206322 89 DQRSRDYGEIARLYRPGHADFTYDAKFGVRDYRGGGRASGRETLSRVAGGAIAQALLAR-HGIAVRAFTVELGGVPADL 166 ***********************************************************.89************99985 PP TIGR00033 159 esakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvsnvpvglGeplfdkldaelasallsinAvK 237 ++++p++ pd++ ++ e+++ ++k +gd++Gg+v+v +++vp+glGep+fdklda la+al+s+ AvK lcl|MicrobesOnline__882:206322 167 VD-----VAGAQQRPFFSPDPDVVEAWEDMVRTVKGEGDTLGGIVQVEATGVPAGLGEPVFDKLDAVLAYALMSVGAVK 240 33.....4568899***************************************************************** PP TIGR00033 238 gveiGdGFeaasvrGseanDelvleddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakat 316 gve+G+GFeaa+++Gs+ nD++v + + tn+ GGi+GGi+nGe i++r+avKpip+i++++ t+d ++k++a lcl|MicrobesOnline__882:206322 241 GVEVGAGFEAARMHGSDNNDPIVPS----GFFTNHAGGILGGISNGETIVLRAAVKPIPSIAQEQITIDRDGKPSALFI 315 **********************965....799*********************************************** PP TIGR00033 317 kgRhDpcvvpravpvvEamvalvladallekr 348 gRhD +++pr+vpv am+alvlad+ll +r lcl|MicrobesOnline__882:206322 316 AGRHDISAIPRIVPVLKAMTALVLADMLLMQR 347 ****************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (354 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: 9.15 // [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