Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_006748504.1 THITH_RS12650 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000227685.2:WP_006748504.1 Length = 375 Score = 542 bits (1397), Expect = e-159 Identities = 262/361 (72%), Positives = 307/361 (85%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M+GN+ G+LF VT FGESHG ALG +VDG PPG+PLTEADLQHDLDRRRPG SR+TTQRR Sbjct: 1 MSGNSFGKLFVVTGFGESHGPALGAVVDGCPPGLPLTEADLQHDLDRRRPGQSRHTTQRR 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 EPD+V+ILSGVFEG TTG IGLLIEN DQRS+DYS I D FRPGHADYTY QKYG+RDY Sbjct: 61 EPDRVRILSGVFEGQTTGAPIGLLIENVDQRSKDYSEIMDRFRPGHADYTYHQKYGVRDY 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQVEQNPFFC 180 RGGGRSSARETAMRVAAG IAK+YL ++G+EIRG L+Q+G IP++ +D S ++ NPFF Sbjct: 121 RGGGRSSARETAMRVAAGGIAKRYLRHRYGVEIRGWLSQLGPIPIEFRDPSAIDSNPFFA 180 Query: 181 PDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMSINAV 240 PDP ++ L+E M AL+K GDS+GA+V V A GVP G GEP+FDRLDADIAHA+MSINAV Sbjct: 181 PDPARVPELEEYMDALRKSGDSVGARVDVEARGVPPGWGEPIFDRLDADIAHAMMSINAV 240 Query: 241 KGVEIGDGFDVVALRGSQNRDEITKDGFQSNHAGGILGGISSGQQIIAHMALKPTSSITV 300 KGVEIGDGF VVA RG+++RDE+T +GF SNH+GG+LGGISSGQ + +ALKPTSSI + Sbjct: 241 KGVEIGDGFGVVAQRGTEHRDEMTPEGFLSNHSGGVLGGISSGQAVRVSIALKPTSSIRL 300 Query: 301 PGRTINRFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQRAQNADVKTDIPR 360 PGRT+N GE VE++T+GRHDPCVGIRA PIAEAMLA+VLMDH LR RAQNADV T IP Sbjct: 301 PGRTVNTSGEAVEVVTRGRHDPCVGIRATPIAEAMLALVLMDHALRHRAQNADVDTGIPA 360 Query: 361 W 361 + Sbjct: 361 Y 361 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: 526 Number of extensions: 16 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: 375 Length adjustment: 30 Effective length of query: 331 Effective length of database: 345 Effective search space: 114195 Effective search space used: 114195 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_006748504.1 THITH_RS12650 (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.26850.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-141 455.4 0.0 6.8e-141 455.2 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006748504.1 THITH_RS12650 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006748504.1 THITH_RS12650 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.2 0.0 6.8e-141 6.8e-141 2 350 .. 11 350 .. 10 351 .. 0.97 Alignments for each domain: == domain 1 score: 455.2 bits; conditional E-value: 6.8e-141 TIGR00033 2 rlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtGa 70 +t fGeSHg+alga++dG+P+gl+lte+d+q++l+rRrpgqsr+t++r+E D+v+ilsGvfeG+TtGa lcl|NCBI__GCF_000227685.2:WP_006748504.1 11 VVTGFGESHGPALGAVVDGCPPGLPLTEADLQHDLDRRRPGQSRHTTQRREPDRVRILSGVFEGQTTGA 79 6899***************************************************************** PP TIGR00033 71 PiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLket 139 Pi lli+N d+rskdy++i +++RPgHadyty +KYg++d++gggrsSaReTa+rvaaG +ak++L++ lcl|NCBI__GCF_000227685.2:WP_006748504.1 80 PIGLLIENVDQRSKDYSEIMDRFRPGHADYTYHQKYGVRDYRGGGRSSARETAMRVAAGGIAKRYLRHR 148 ********************************************************************* PP TIGR00033 140 agieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvvs 208 +g+ei +++++lg + +e++ + ++d++p+++pd+ + e+ee++d ++k+gdsvG++v+v ++ lcl|NCBI__GCF_000227685.2:WP_006748504.1 149 YGVEIRGWLSQLGPIPIEFRD-----PSAIDSNPFFAPDPARVPELEEYMDALRKSGDSVGARVDVEAR 212 ***************999743.....668**************************************** PP TIGR00033 209 nvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGie 277 +vp g+Gep+fd+lda +a+a++sinAvKgveiGdGF + +rG e+ De++ e + +n+sGG++ lcl|NCBI__GCF_000227685.2:WP_006748504.1 213 GVPPGWGEPIFDRLDADIAHAMMSINAVKGVEIGDGFGVVAQRGTEHRDEMTPE----GFLSNHSGGVL 277 *************************************************88654....69********* PP TIGR00033 278 GGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladalle 346 GGi+ G+ +rv+ia+Kp+++i+ p +tv+++++ +t+gRhDpcv +ra+p++Eam+alvl+d++l+ lcl|NCBI__GCF_000227685.2:WP_006748504.1 278 GGISSGQAVRVSIALKPTSSIRLPGRTVNTSGEAVEVVTRGRHDPCVGIRATPIAEAMLALVLMDHALR 346 ******************************999999999****************************** PP TIGR00033 347 kras 350 +ra+ lcl|NCBI__GCF_000227685.2:WP_006748504.1 347 HRAQ 350 *987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (375 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.10 // [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