Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate Synpcc7942_0212 Synpcc7942_0212 chorismate synthase
Query= BRENDA::B5AAU3 (442 letters) >FitnessBrowser__SynE:Synpcc7942_0212 Length = 362 Score = 483 bits (1242), Expect = e-141 Identities = 237/361 (65%), Positives = 282/361 (78%), Gaps = 3/361 (0%) Query: 55 GNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKET 114 G+ FG F+++T+GESHGGGVG VI GCPPR+ ++E ++Q +LDRRRPGQS+ITTPRKE Sbjct: 2 GSSFGHLFRISTFGESHGGGVGVVIDGCPPRLEISEAEIQFELDRRRPGQSKITTPRKEA 61 Query: 115 DTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQG 174 D C+ILSG +G T GTPI + V N DQR DY+EM AYRPSHAD TYD KYG+R+V G Sbjct: 62 DQCEILSGVVDGKTLGTPIAIVVRNKDQRSQDYSEMQVAYRPSHADATYDAKYGIRAVAG 121 Query: 175 GGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIES 234 GGRSSARETIGRVAAGA+AKK+L+ GVEI+ +V ++ + E +D ET+TL+Q+ES Sbjct: 122 GGRSSARETIGRVAAGAIAKKLLREIAGVEIVGYVKRIKDL---EGQIDPETVTLEQVES 178 Query: 235 NICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAML 294 I RCPD A +MID I+ + G+S+GGVV C+AR VPRGLG PVFDKLEA LAKA + Sbjct: 179 TIVRCPDEAIAPQMIDLIEAIGREGDSLGGVVECVARRVPRGLGEPVFDKLEADLAKACM 238 Query: 295 SLPASKGFEIGSGFAGTDLTGSEHNDEFYMDEGGNVRTRTNRSGGVQGGISNGETIYFKV 354 SLPA+KGFEIGSGFAGT++TGSEHND FY DE G +RTRTNRSGG QGGISNGE I +V Sbjct: 239 SLPATKGFEIGSGFAGTEMTGSEHNDAFYTDEQGQIRTRTNRSGGTQGGISNGENIVIRV 298 Query: 355 AFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAHVAQ 414 AFKPTATI K+Q TVT E L RGRHDPCV+PRAVPMVE M ALVL D L+ AQ Sbjct: 299 AFKPTATIRKEQETVTNSGEATTLAARGRHDPCVLPRAVPMVEAMVALVLCDHLLRQQAQ 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: 489 Number of extensions: 12 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: 362 Length adjustment: 31 Effective length of query: 411 Effective length of database: 331 Effective search space: 136041 Effective search space used: 136041 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 Synpcc7942_0212 Synpcc7942_0212 (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.4739.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-145 469.7 1.4 2.9e-145 469.6 1.4 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0212 Synpcc7942_0212 chorismate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0212 Synpcc7942_0212 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.6 1.4 2.9e-145 2.9e-145 1 349 [. 9 357 .. 9 359 .. 0.98 Alignments for each domain: == domain 1 score: 469.6 bits; conditional E-value: 2.9e-145 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 +r+ tfGeSHg +g++idG+P+ le++e++iq el+rRrpgqs+ t++rkE+D+ eilsGv GkT G lcl|FitnessBrowser__SynE:Synpcc7942_0212 9 FRISTFGESHGGGVGVVIDGCPPRLEISEAEIQFELDRRRPGQSKITTPRKEADQCEILSGVVDGKTLG 77 7999***************************************************************** PP TIGR00033 70 aPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklLke 138 +Pia++++Nkd+rs+dy++++ +RP+Had ty KYgi++ gggrsSaReT++rvaaGa+akklL+e lcl|FitnessBrowser__SynE:Synpcc7942_0212 78 TPIAIVVRNKDQRSQDYSEMQVAYRPSHADATYDAKYGIRAVAGGGRSSARETIGRVAAGAIAKKLLRE 146 ********************************************************************* PP TIGR00033 139 tagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgvvevvv 207 ag+eiv+yv ++ ++e + ++++ e+++++ vrcpd+ + +m ++i+ + ++gds+Ggvve+v+ lcl|FitnessBrowser__SynE:Synpcc7942_0212 147 IAGVEIVGYVKRIKDLEGQI-DPETVTLEQVESTIVRCPDEAIAPQMIDLIEAIGREGDSLGGVVECVA 214 *****************996.5556899***************************************** PP TIGR00033 208 snvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle.ddkirrktnnsGG 275 + vp glGep+fdkl+a la+a +s++A Kg+eiG+GF+ ++++Gse+nD ++++ +++ir++tn+sGG lcl|FitnessBrowser__SynE:Synpcc7942_0212 215 RRVPRGLGEPVFDKLEADLAKACMSLPATKGFEIGSGFAGTEMTGSEHNDAFYTDeQGQIRTRTNRSGG 283 ******************************************************9899*********** PP TIGR00033 276 ieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEamvalvladal 344 ++GGi+nGe+i++r+a+Kp++ti+k+++tv+ +++ ++ a++gRhDpcv+pravp+vEamvalvl d+l lcl|FitnessBrowser__SynE:Synpcc7942_0212 284 TQGGISNGENIVIRVAFKPTATIRKEQETVTNSGEATTLAARGRHDPCVLPRAVPMVEAMVALVLCDHL 352 *********************************99999999**************************** PP TIGR00033 345 lekra 349 l+++a lcl|FitnessBrowser__SynE:Synpcc7942_0212 353 LRQQA 357 *9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (362 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: 10.24 // [ok]
This GapMind analysis is from Apr 09 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