Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013682925.1 ARCVE_RS01035 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000194625.1:WP_013682925.1 Length = 365 Score = 353 bits (905), Expect = e-102 Identities = 182/358 (50%), Positives = 250/358 (69%), Gaps = 13/358 (3%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 M GNT G +FRVTT+GESHG A+GC+VDG P G+ ++ +Q +LDRR+PG R T+R+ Sbjct: 1 MVGNTFGHIFRVTTWGESHGKAVGCVVDGCPAGLDISSEVIQRELDRRKPG-GRLATKRK 59 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D+V+ILSGVFEG T GT I +LI N D S+ Y IKD+ RPGHADYTY K+G+RD+ Sbjct: 60 EEDKVEILSGVFEGKTLGTPISMLIWNKDVDSRPYEEIKDLLRPGHADYTYLAKFGIRDW 119 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWS------QVE 174 RGGGR+SARETA RVAAGAIAK LA +FG+++ G ++ + ++ S + E Sbjct: 120 RGGGRASARETAARVAAGAIAKHLLA-RFGVKVGGYAKEIAGVSCNVDGMSFEEIVEKAE 178 Query: 175 QNPFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHAL 234 ++ CPD + ++E + ++EGDS+G V V+ PAGLGEPVF +LDA IA+A+ Sbjct: 179 KSDVRCPDSEAAKLMEERIIEARREGDSVGGVVEVIVKNPPAGLGEPVFMKLDAYIAYAV 238 Query: 235 MSINAVKGVEIGDGFDVVALRGSQNRDEIT----KDGFQSNHAGGILGGISSGQQIIAHM 290 M I AVKGVEIG GF+ ++GS++ D I + GF +N+AGGILGG+S+G II Sbjct: 239 MGIPAVKGVEIGAGFEAARMKGSEHNDPIVIKNGRIGFATNNAGGILGGVSNGDDIIVRA 298 Query: 291 ALKPTSSITVPGRTIN-RFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLRQ 347 A+KPT SI+ P RT+N R +E E++ KGRHDPC+ RAVP+ EAM+++ + D ++ Q Sbjct: 299 AIKPTPSISKPQRTVNFRTMKEEEIVVKGRHDPCIVPRAVPVVEAMVSLAIADAMMLQ 356 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: 372 Number of extensions: 19 Number of successful extensions: 7 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: 365 Length adjustment: 29 Effective length of query: 332 Effective length of database: 336 Effective search space: 111552 Effective search space used: 111552 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_013682925.1 ARCVE_RS01035 (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.15431.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-151 487.7 1.2 1e-150 487.5 1.2 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013682925.1 ARCVE_RS01035 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013682925.1 ARCVE_RS01035 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.5 1.2 1e-150 1e-150 1 347 [. 10 356 .. 10 359 .. 0.98 Alignments for each domain: == domain 1 score: 487.5 bits; conditional E-value: 1e-150 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHgka+g+++dG+Pagl ++ e iq+el+rR+pg rl+++rkEeD+veilsGvfeGkT G lcl|NCBI__GCF_000194625.1:WP_013682925.1 10 FRVTTWGESHGKAVGCVVDGCPAGLDISSEVIQRELDRRKPGG-RLATKRKEEDKVEILSGVFEGKTLG 77 89****************************************6.************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi++li Nkdv+s++ye+ik+l RPgHadytyl K+gi+d +gggr+SaReTaarvaaGa+ak+lL++ lcl|NCBI__GCF_000194625.1:WP_013682925.1 78 TPISMLIWNKDVDSRPYEEIKDLLRPGHADYTYLAKFGIRDWRGGGRASARETAARVAAGAIAKHLLAR 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevv 206 g+++ +y +++ v+++ + ++ e++ e+++ks vrcpd ea+k mee i +a+++gdsvGgvvev+ lcl|NCBI__GCF_000194625.1:WP_013682925.1 147 -FGVKVGGYAKEIAGVSCNVDGMSfEEIVEKAEKSDVRCPDSEAAKLMEERIIEARREGDSVGGVVEVI 214 .88***************99999888899**************************************** PP TIGR00033 207 vsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGG 275 v+n p+glGep+f klda +a+a+++i+AvKgveiG+GFeaa+++Gse+nD++v+++++i + tnn GG lcl|NCBI__GCF_000194625.1:WP_013682925.1 215 VKNPPAGLGEPVFMKLDAYIAYAVMGIPAVKGVEIGAGFEAARMKGSEHNDPIVIKNGRIGFATNNAGG 283 ********************************************************************* PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvlada 343 i+GG++nG di vr+a+Kp+p+i+kp++tv+ +t+++ ++ kgRhDpc+vpravpvvEamv+l +ada lcl|NCBI__GCF_000194625.1:WP_013682925.1 284 ILGGVSNGDDIIVRAAIKPTPSISKPQRTVNFRTMKEEEIVvKGRHDPCIVPRAVPVVEAMVSLAIADA 352 **********************************99999988*************************** PP TIGR00033 344 llek 347 ++ + lcl|NCBI__GCF_000194625.1:WP_013682925.1 353 MMLQ 356 9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (365 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: 7.43 // [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