Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_013461375.1 SULKU_RS12715 chorismate synthase
Query= SwissProt::P56122 (365 letters) >NCBI__GCF_000183725.1:WP_013461375.1 Length = 357 Score = 410 bits (1053), Expect = e-119 Identities = 206/362 (56%), Positives = 262/362 (72%), Gaps = 6/362 (1%) Query: 1 MNTLGRFLRLTTFGESHGDVIGGVLDGMPSGIKIDYALLENEMKRRQGGRNVFITPRKED 60 MN G +TTFGESHG IG VLDG+P+G+ ID +++E+ RR+ G+N F T RKE Sbjct: 1 MNRFGERFTITTFGESHGKAIGCVLDGVPAGLLIDEDYIQSELDRRKPGQNEFATARKEA 60 Query: 61 DKVEITSGVFEDFSTGTPIGFLIHNQRARSKDYDNIKNLFRPSHADFTYFHKYGIRDFRG 120 D VEI SGVFE STGTPI +I+N +S DY N+K++FRP HADFTYFHKYG+RD+RG Sbjct: 61 DCVEILSGVFEGLSTGTPIMMVIYNTDQKSGDYSNVKDIFRPGHADFTYFHKYGLRDYRG 120 Query: 121 GGRSSARESAIRVAAGAFAKMLLREIGIVCESGIIEIGGIKAKNYDFNHALKSEIFALDE 180 GGRSSARE+A RVA GA AK++L ++GI +SGI I GI+A++ DF + S I+ALD Sbjct: 121 GGRSSARETAARVAGGAVAKLMLSQLGITFQSGISAIHGIEAQSLDFTYPQNSPIYALDA 180 Query: 181 EQEEAQKTAIQNAIKNHDSIGGVALIRARSIKTNQKLPIGLGQGLYAKLDAKIAEAMMGL 240 EEAQK AI A +HDS+GGV ++ LPIGLG+GLY KLDA +AEAMMG+ Sbjct: 181 SVEEAQKAAILEAKNSHDSVGGVCTVKISG------LPIGLGEGLYYKLDAVLAEAMMGI 234 Query: 241 NGVKAVEIGKGVESSLLKGSEYNDLMDQKGFLSNRSGGVLGGMSNGEEIIVRVHFKPTPS 300 N VKAVEIG+G+ S L S+ ND + KGF +N +GG+LGGMSNG++++VRVHFKPTPS Sbjct: 235 NAVKAVEIGEGIRSGELLASQNNDAITPKGFKTNHAGGILGGMSNGDDVLVRVHFKPTPS 294 Query: 301 IFQPQRTIDINGNECECLLKGRHDPCIAIRGSVVCESLLALVLADMVLLNLTSKIEYLKT 360 IF Q +++ LKGRHDPC+A+RGSVV ES+ ALV ADMVLLN+ S + +K Sbjct: 295 IFIDQESVNTENESVNVSLKGRHDPCVAVRGSVVAESMAALVCADMVLLNMGSTMNGIKG 354 Query: 361 IY 362 Y Sbjct: 355 YY 356 Lambda K H 0.319 0.139 0.395 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: 425 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: 365 Length of database: 357 Length adjustment: 29 Effective length of query: 336 Effective length of database: 328 Effective search space: 110208 Effective search space used: 110208 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_013461375.1 SULKU_RS12715 (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.19760.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-123 397.6 0.6 2.6e-123 397.4 0.6 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013461375.1 SULKU_RS12715 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013461375.1 SULKU_RS12715 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.4 0.6 2.6e-123 2.6e-123 1 348 [. 8 345 .. 8 348 .. 0.95 Alignments for each domain: == domain 1 score: 397.4 bits; conditional E-value: 2.6e-123 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +++ttfGeSHgka+g+++dG+Pagl ++e++iq+el+rR+pgq ++++ rkE+D veilsGvfeG tG lcl|NCBI__GCF_000183725.1:WP_013461375.1 8 FTITTFGESHGKAIGCVLDGVPAGLLIDEDYIQSELDRRKPGQNEFATARKEADCVEILSGVFEGLSTG 76 789****************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi ++i+N+d++s dy+++k+++RPgHad+ty++KYg++d++gggrsSaReTaarva Gavak +L++ lcl|NCBI__GCF_000183725.1:WP_013461375.1 77 TPIMMVIYNTDQKSGDYSNVKDIFRPGHADFTYFHKYGLRDYRGGGRSSARETAARVAGGAVAKLMLSQ 145 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 gi + ++ + +e+++ ++ ++sp+ ++da+ e++ ++ i +ak+++dsvGgv +v + lcl|NCBI__GCF_000183725.1:WP_013461375.1 146 -LGITFQSGISAIHGIEAQSLDFT-----YPQNSPIYALDASVEEAQKAAILEAKNSHDSVGGVCTVKI 208 .88*****9999999999975554.....35669*********************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvleddkirrktnnsGGi 276 s++p glGe l+ klda la+a+++inAvK+veiG+G ++ + s+ nD + + +ktn+ GGi lcl|NCBI__GCF_000183725.1:WP_013461375.1 209 SGLPIGLGEGLYYKLDAVLAEAMMGINAVKAVEIGEGIRSGELLASQNNDAI----TPKGFKTNHAGGI 273 **************************************************66....45679******** PP TIGR00033 277 eGGitnGedirvriavKpiptikkplktvdletkekakat.kgRhDpcvvpravpvvEamvalvladal 344 +GG++nG d+ vr+ +Kp+p+i ++++v++ ++e+++++ kgRhDpcv++r ++v+E+m alv ad++ lcl|NCBI__GCF_000183725.1:WP_013461375.1 274 LGGMSNGDDVLVRVHFKPTPSIFIDQESVNT-ENESVNVSlKGRHDPCVAVRGSVVAESMAALVCADMV 341 ******************************9.566777777***************************9 PP TIGR00033 345 lekr 348 l ++ lcl|NCBI__GCF_000183725.1:WP_013461375.1 342 LLNM 345 9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (357 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: 10.41 // [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