Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate WP_009543726.1 CCE_RS19810 chorismate synthase
Query= BRENDA::B5AAU3 (442 letters) >NCBI__GCF_000017845.1:WP_009543726.1 Length = 363 Score = 498 bits (1282), Expect = e-145 Identities = 241/363 (66%), Positives = 293/363 (80%), Gaps = 3/363 (0%) Query: 55 GNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKET 114 GN FG F++ T+GESHGGGVG +I GCPPR+ L+E D+QGDLDRRRPGQS+ITTPRKET Sbjct: 2 GNTFGHLFRITTFGESHGGGVGVIIDGCPPRLDLSESDIQGDLDRRRPGQSKITTPRKET 61 Query: 115 DTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQG 174 DTC+I+SG ++G T GTPI + V N D R DY EM+ +RPSHAD TY+ KYG+R+ QG Sbjct: 62 DTCEIISGVFQGKTLGTPIAILVRNKDARSQDYNEMSVKFRPSHADATYEAKYGIRNWQG 121 Query: 175 GGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIES 234 GGRSSARETIGRVAAGA+AKKILK VEI+ +V ++ + E V+ +T+TL+++ES Sbjct: 122 GGRSSARETIGRVAAGAIAKKILKQVANVEIVGYVKRIKDL---EGNVNPDTVTLEEVES 178 Query: 235 NICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAML 294 NI RCPD + A+KMID ID+ R + +SIGGVV C+AR VPRGLG PVFDKLEA LAKA++ Sbjct: 179 NIVRCPDADMAEKMIDLIDQTRRDKDSIGGVVECVARYVPRGLGEPVFDKLEADLAKAVM 238 Query: 295 SLPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKV 354 SLPASKGFEIGSGFAGT LTGSEHNDEFY+D+ GN+RT+TNRSGG+QGGISNGE I +V Sbjct: 239 SLPASKGFEIGSGFAGTLLTGSEHNDEFYIDDNGNIRTKTNRSGGIQGGISNGEHIIIRV 298 Query: 355 AFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAHVAQ 414 AFKPTATIGK+Q TVT + E+ L +GRHDPCV+ RAVPMVE M ALVL D L+ Q Sbjct: 299 AFKPTATIGKEQKTVTSESEETTLAAKGRHDPCVLSRAVPMVEAMVALVLCDHLLRWQGQ 358 Query: 415 CEM 417 C++ Sbjct: 359 CQV 361 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: 502 Number of extensions: 10 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: 442 Length of database: 363 Length adjustment: 31 Effective length of query: 411 Effective length of database: 332 Effective search space: 136452 Effective search space used: 136452 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_009543726.1 CCE_RS19810 (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.26287.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-150 485.6 0.6 4.6e-150 485.4 0.6 1.0 1 lcl|NCBI__GCF_000017845.1:WP_009543726.1 CCE_RS19810 chorismate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017845.1:WP_009543726.1 CCE_RS19810 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.4 0.6 4.6e-150 4.6e-150 1 347 [. 9 355 .. 9 359 .. 0.98 Alignments for each domain: == domain 1 score: 485.4 bits; conditional E-value: 4.6e-150 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ttfGeSHg +g+iidG+P+ l l+e+diq +l+rRrpgqs+ t++rkE+D+ ei+sGvf+GkT G lcl|NCBI__GCF_000017845.1:WP_009543726.1 9 FRITTFGESHGGGVGVIIDGCPPRLDLSESDIQGDLDRRRPGQSKITTPRKETDTCEIISGVFQGKTLG 77 89******************************************************************* PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pia+l++Nkd rs+dy++++ ++RP+Had ty+ KYgi++ +gggrsSaReT++rvaaGa+akk Lk+ lcl|NCBI__GCF_000017845.1:WP_009543726.1 78 TPIAILVRNKDARSQDYNEMSVKFRPSHADATYEAKYGIRNWQGGGRSSARETIGRVAAGAIAKKILKQ 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 a++eiv+yv ++ ++e + + ++++ e+++++ vrcpda+ +++m ++id+ ++d+ds+Ggvve+v+ lcl|NCBI__GCF_000017845.1:WP_009543726.1 147 VANVEIVGYVKRIKDLEGNV-NPDTVTLEEVESNIVRCPDADMAEKMIDLIDQTRRDKDSIGGVVECVA 214 ******************95.667789****************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275 + vp glGep+fdkl+a la+a++s++A Kg+eiG+GF+ + +Gse+nDe++++ +++ir+ktn+sGG lcl|NCBI__GCF_000017845.1:WP_009543726.1 215 RYVPRGLGEPVFDKLEADLAKAVMSLPASKGFEIGSGFAGTLLTGSEHNDEFYIDdNGNIRTKTNRSGG 283 *******************************************************8899********** PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344 i+GGi+nGe+i +r+a+Kp++ti+k++ktv+ e +e++ a+kgRhDpcv+ ravp+vEamvalvl d+l lcl|NCBI__GCF_000017845.1:WP_009543726.1 284 IQGGISNGEHIIIRVAFKPTATIGKEQKTVTSESEETTLAAKGRHDPCVLSRAVPMVEAMVALVLCDHL 352 ********************************************************************* PP TIGR00033 345 lek 347 l+ lcl|NCBI__GCF_000017845.1:WP_009543726.1 353 LRW 355 975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (363 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: 7.69 // [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