Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EPSP phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_011033654.1 MM_RS08880 chorismate synthase
Query= SwissProt::P12008 (361 letters) >NCBI__GCF_000007065.1:WP_011033654.1 Length = 365 Score = 362 bits (930), Expect = e-105 Identities = 193/355 (54%), Positives = 250/355 (70%), Gaps = 10/355 (2%) Query: 1 MAGNTIGQLFRVTTFGESHGLALGCIVDGVPPGIPLTEADLQHDLDRRRPGTSRYTTQRR 60 MAGN GQ+FR+TT+GESHG A+G +VDG+P G+P +EAD+Q +LDRRRPG S +T R Sbjct: 1 MAGNVFGQMFRITTWGESHGRAVGVVVDGLPAGLPFSEADIQKELDRRRPGQSEVSTPRS 60 Query: 61 EPDQVKILSGVFEGVTTGTSIGLLIENTDQRSQDYSAIKDVFRPGHADYTYEQKYGLRDY 120 E D V+ILSG+FEG +TGT I +L+ N+D RS Y AIK+ RPGHAD+TY +YG+RD+ Sbjct: 61 EADSVEILSGIFEGKSTGTPISMLVWNSDARSSSYDAIKNTPRPGHADFTYIARYGIRDH 120 Query: 121 RGGGRSSARETAMRVAAGAIAKKYLAEKFGIEIRGCLTQMGDIPLDIKDWSQ----VEQN 176 RGGGRSSARET RVA GA+AK L+ +GI I G + ++G I + + VE+ Sbjct: 121 RGGGRSSARETIGRVAGGALAKLLLSH-YGIRIVGHVLELGGIRAKSLSFEEILENVERT 179 Query: 177 PFFCPDPDKIDALDELMRALKKEGDSIGAKVTVVASGVPAGLGEPVFDRLDADIAHALMS 236 P C DP+ + E + AL++EGDS G V V+ GVPAGLGEPVFDRLDAD+A ALMS Sbjct: 180 PVRCADPEAAKKMLEKVSALRQEGDSAGGIVEVMVKGVPAGLGEPVFDRLDADLAKALMS 239 Query: 237 INAVKGVEIGDGFDVVALRGSQNRDE-ITKDG---FQSNHAGGILGGISSGQQIIAHMAL 292 I AVKG EIG GF+ +RGS+ D + +DG SN+AGGILGGISSG I+ +A+ Sbjct: 240 IPAVKGFEIGAGFEAARMRGSEMNDSFLMEDGKVTCSSNNAGGILGGISSGLDIVCRVAV 299 Query: 293 KPTSSITVPGRTIN-RFGEEVEMITKGRHDPCVGIRAVPIAEAMLAIVLMDHLLR 346 KPT SI+ +T++ E E+ KGRHDP + R VP+AEAM+A+V DH+LR Sbjct: 300 KPTPSISKLQQTVDLTTRENAEIAIKGRHDPTIPPRMVPVAEAMVALVFADHMLR 354 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: 380 Number of extensions: 16 Number of successful extensions: 5 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_011033654.1 MM_RS08880 (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.5380.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-149 484.0 0.1 1.3e-149 483.8 0.1 1.0 1 lcl|NCBI__GCF_000007065.1:WP_011033654.1 MM_RS08880 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_011033654.1 MM_RS08880 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 483.8 0.1 1.3e-149 1.3e-149 1 349 [. 10 357 .. 10 359 .. 0.99 Alignments for each domain: == domain 1 score: 483.8 bits; conditional E-value: 1.3e-149 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+tt+GeSHg+a+g+++dGlPagl+ +e+diqkel+rRrpgqs+++++r+E+D+veilsG+feGk tG lcl|NCBI__GCF_000007065.1:WP_011033654.1 10 FRITTWGESHGRAVGVVVDGLPAGLPFSEADIQKELDRRRPGQSEVSTPRSEADSVEILSGIFEGKSTG 78 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi++l+ N d rs+ y+ ik++pRPgHad+ty +Ygi+d++gggrsSaReT++rva Ga+ak lL++ lcl|NCBI__GCF_000007065.1:WP_011033654.1 79 TPISMLVWNSDARSSSYDAIKNTPRPGHADFTYIARYGIRDHRGGGRSSARETIGRVAGGALAKLLLSH 147 *******************************************************************99 PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +gi+iv++v +lg +++++ s++e + e+++++pvrc+d+ea+k+m e ++ ++++gds Gg+vev+v lcl|NCBI__GCF_000007065.1:WP_011033654.1 148 -YGIRIVGHVLELGGIRAKSLSFEE-ILENVERTPVRCADPEAAKKMLEKVSALRQEGDSAGGIVEVMV 214 .99****************999987.8899*************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 ++vp+glGep+fd+lda la+al+si+AvKg+eiG+GFeaa++rGse+nD + +ed+k++ +nn GGi lcl|NCBI__GCF_000007065.1:WP_011033654.1 215 KGVPAGLGEPVFDRLDADLAKALMSIPAVKGFEIGAGFEAARMRGSEMNDSFLMEDGKVTCSSNNAGGI 283 ********************************************************************* PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvladal 344 +GGi+ G di+ r+avKp+p+i+k ++tvdl+t+e+a+++ kgRhDp++ pr vpv+Eamvalv+ad++ lcl|NCBI__GCF_000007065.1:WP_011033654.1 284 LGGISSGLDIVCRVAVKPTPSISKLQQTVDLTTRENAEIAiKGRHDPTIPPRMVPVAEAMVALVFADHM 352 ****************************************9**************************** PP TIGR00033 345 lekra 349 l++ + lcl|NCBI__GCF_000007065.1:WP_011033654.1 353 LRSGF 357 *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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.15 // [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