Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate WP_011612398.1 TERY_RS13785 chorismate synthase
Query= BRENDA::B5AAU3 (442 letters) >NCBI__GCF_000014265.1:WP_011612398.1 Length = 370 Score = 486 bits (1251), Expect = e-142 Identities = 235/361 (65%), Positives = 289/361 (80%), Gaps = 3/361 (0%) Query: 55 GNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKET 114 GNIFG F+V T+GESHGGGVG +I GCPP++ + +++Q +LDRRRPGQS+ITTPRKE+ Sbjct: 2 GNIFGHLFRVTTFGESHGGGVGVIIDGCPPKLEINVKEIQYELDRRRPGQSKITTPRKES 61 Query: 115 DTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQG 174 DTC+ILSG +EG T GTPI ++V N D R DY +MA YRPSHAD TYD KYG+R+ QG Sbjct: 62 DTCEILSGVFEGQTLGTPIMIWVRNKDARPQDYQDMAIKYRPSHADATYDAKYGIRNWQG 121 Query: 175 GGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIES 234 GGRSSARETIGRVA+GA+AKKIL+ GVEI+ +V ++ + E VD T+T++Q+ES Sbjct: 122 GGRSSARETIGRVASGAIAKKILQQYSGVEIVGYVKRIKNL---EAIVDPTTVTMEQVES 178 Query: 235 NICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAML 294 NI RCPD E A+KMI+ ++K+R G+S+GGVV CI RNVP+GLGSPVFDKLEA LAK ++ Sbjct: 179 NIVRCPDSECAEKMIELVEKIRDLGDSVGGVVECIVRNVPKGLGSPVFDKLEADLAKGVM 238 Query: 295 SLPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKV 354 SLPA+KGFEIGSGFAGT +TGSEHNDE Y D+ G +RT TNRSGG+QGGISNGE I +V Sbjct: 239 SLPATKGFEIGSGFAGTTMTGSEHNDELYTDKLGEIRTVTNRSGGIQGGISNGENIVLRV 298 Query: 355 AFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAHVAQ 414 AFKPTATI K+Q TV+R E+ L +GRHDPCV+PRAVPMVE M A+VL D L+ H Q Sbjct: 299 AFKPTATIRKEQRTVSRQGEETFLAAKGRHDPCVLPRAVPMVEAMVAIVLCDHLLRHYGQ 358 Query: 415 C 415 C Sbjct: 359 C 359 Lambda K H 0.317 0.135 0.396 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: 497 Number of extensions: 13 Number of successful extensions: 3 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: 442 Length of database: 370 Length adjustment: 31 Effective length of query: 411 Effective length of database: 339 Effective search space: 139329 Effective search space used: 139329 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_011612398.1 TERY_RS13785 (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.23498.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-146 473.3 0.6 2.5e-146 473.1 0.6 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011612398.1 TERY_RS13785 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011612398.1 TERY_RS13785 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.1 0.6 2.5e-146 2.5e-146 1 349 [. 9 357 .. 9 359 .. 0.99 Alignments for each domain: == domain 1 score: 473.1 bits; conditional E-value: 2.5e-146 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHg +g+iidG+P+ le++ ++iq el+rRrpgqs+ t++rkE+D+ eilsGvfeG+T G lcl|NCBI__GCF_000014265.1:WP_011612398.1 9 FRVTTFGESHGGGVGVIIDGCPPKLEINVKEIQYELDRRRPGQSKITTPRKESDTCEILSGVFEGQTLG 77 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pi + ++Nkd r++dy+d++ ++RP+Had ty KYgi++ +gggrsSaReT++rva+Ga+akk L++ lcl|NCBI__GCF_000014265.1:WP_011612398.1 78 TPIMIWVRNKDARPQDYQDMAIKYRPSHADATYDAKYGIRNWQGGGRSSARETIGRVASGAIAKKILQQ 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 +g+eiv+yv ++ ++e+ + ++ ++ e+++++ vrcpd e++++m e+++k+++ gdsvGgvve++v lcl|NCBI__GCF_000014265.1:WP_011612398.1 147 YSGVEIVGYVKRIKNLEAIVDPTT-VTMEQVESNIVRCPDSECAEKMIELVEKIRDLGDSVGGVVECIV 214 ****************99976666.79****************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275 +nvp glG+p+fdkl+a la+ ++s++A Kg+eiG+GF+ ++++Gse+nDel+++ ++ir++tn+sGG lcl|NCBI__GCF_000014265.1:WP_011612398.1 215 RNVPKGLGSPVFDKLEADLAKGVMSLPATKGFEIGSGFAGTTMTGSEHNDELYTDkLGEIRTVTNRSGG 283 *******************************************************99************ PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344 i+GGi+nGe+i++r+a+Kp++ti+k+++tv +++e+ a+kgRhDpcv+pravp+vEamva+vl d+l lcl|NCBI__GCF_000014265.1:WP_011612398.1 284 IQGGISNGENIVLRVAFKPTATIRKEQRTVSRQGEETFLAAKGRHDPCVLPRAVPMVEAMVAIVLCDHL 352 ********************************************************************* PP TIGR00033 345 lekra 349 l++ + lcl|NCBI__GCF_000014265.1:WP_011612398.1 353 LRHYG 357 *9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (370 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.36 // [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