Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate CA265_RS11645 CA265_RS11645 chorismate synthase
Query= BRENDA::B5AAU3 (442 letters) >FitnessBrowser__Pedo557:CA265_RS11645 Length = 365 Score = 370 bits (950), Expect = e-107 Identities = 192/362 (53%), Positives = 245/362 (67%), Gaps = 3/362 (0%) Query: 54 AGNIFGDYFQVATYGESHGGGVGCVISGCPPRIPLTEEDMQGDLDRRRPGQSRITTPRKE 113 AGN FG F++ T+GESHG +G +I GCP ++ + + +Q +LD+R+PGQS+ITT RKE Sbjct: 2 AGNSFGQLFRITTFGESHGVAIGVIIDGCPAQLDIDMDFIQSELDKRKPGQSKITTQRKE 61 Query: 114 TDTCKILSGTYEGMTTGTPIHVFVPNTDQRGGDYTEMAKAYRPSHADLTYDLKYGVRSVQ 173 +DT +ILSG +EG +TGTPI + +PN DQR DY YRPSHAD YD KYG+R + Sbjct: 62 SDTVQILSGVFEGKSTGTPIALLIPNEDQRSKDYGHNVDVYRPSHADYVYDAKYGIRDHR 121 Query: 174 GGGRSSARETIGRVAAGAVAKKILKLKCGVEILAFVSKVHQVVLPEDAVDYETLTLDQIE 233 GGGRSSARET RVAAGA+AK LK + G+EI A V+ V + P + + L E Sbjct: 122 GGGRSSARETAARVAAGAIAKLFLKQQ-GIEIFAHVTSVGTIEAPNLESNDLSALLQIRE 180 Query: 234 SNICRCPDPEYAQKMIDAIDKVRINGNSIGGVVTCIARNVPRGLGSPVFDKLEALLAKAM 293 NI RC DP A +MI+ ID VR +G+++GG + C+ + P GLG PVFDKL A L KAM Sbjct: 181 ENIVRCADPATAHEMIEFIDSVRKDGDTVGGKIGCVVKGCPAGLGEPVFDKLHADLGKAM 240 Query: 294 LSLPASKGFEIGSGFAGTDLTGSEHND--EFYMDEGGNVRTRTNRSGGVQGGISNGETIY 351 LS+ A GFE GSGFAG++L GS+HND + + +T TN +GG+ GGISNG I Sbjct: 241 LSINAVHGFEYGSGFAGSELRGSQHNDIPQPKAADSKVFKTTTNYAGGILGGISNGMDIT 300 Query: 352 FKVAFKPTATIGKKQNTVTRDHEDIELLTRGRHDPCVVPRAVPMVETMAALVLMDQLMAH 411 FKVAFKP ATI Q T+ E E+ +GRHDPCVVPRAV +VE MAALVL DQ + + Sbjct: 301 FKVAFKPVATIMHNQQTINAAGEASEIKGKGRHDPCVVPRAVVIVEAMAALVLADQFLRN 360 Query: 412 VA 413 A Sbjct: 361 KA 362 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: 436 Number of extensions: 23 Number of successful extensions: 4 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: 365 Length adjustment: 31 Effective length of query: 411 Effective length of database: 334 Effective search space: 137274 Effective search space used: 137274 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 CA265_RS11645 CA265_RS11645 (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.10191.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-141 457.2 1.2 1.9e-141 457.1 1.2 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS11645 CA265_RS11645 chorismate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS11645 CA265_RS11645 chorismate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.1 1.2 1.9e-141 1.9e-141 1 349 [. 10 362 .. 10 364 .. 0.95 Alignments for each domain: == domain 1 score: 457.1 bits; conditional E-value: 1.9e-141 TIGR00033 1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTt 68 +r+ttfGeSHg a+g+iidG+Pa l ++++ iq+el++R+pgqs+ t++rkE+D+v+ilsGvfeGk t lcl|FitnessBrowser__Pedo557:CA265_RS11645 10 FRITTFGESHGVAIGVIIDGCPAQLDIDMDFIQSELDKRKPGQSKITTQRKESDTVQILSGVFEGKST 77 89****************************************************************** PP TIGR00033 69 GaPiallikNkdvrskdyedikelpRPgHadytylkKYgikdregggrsSaReTaarvaaGavakklL 136 G+Pialli N+d+rskdy + +++RP+Hady+y KYgi+d++gggrsSaReTaarvaaGa+ak +L lcl|FitnessBrowser__Pedo557:CA265_RS11645 78 GTPIALLIPNEDQRSKDYGHNVDVYRPSHADYVYDAKYGIRDHRGGGRSSARETAARVAAGAIAKLFL 145 ******************************************************************** PP TIGR00033 137 ketagieivayvvklgeveleeesak..eiskerldkspvrcpdaeaekemeeeidkakkdgdsvGgv 202 k+ +giei a+v+++g +e+++ + + + + +++ vrc+d+ +++em e id+++kdgd+vGg+ lcl|FitnessBrowser__Pedo557:CA265_RS11645 146 KQ-QGIEIFAHVTSVGTIEAPNLESNdlSALLQIREENIVRCADPATAHEMIEFIDSVRKDGDTVGGK 212 **.99***************98777756556778888******************************* PP TIGR00033 203 vevvvsnvpvglGeplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle...ddkir 267 + +vv++ p+glGep+fdkl+a l++a+lsinAv g+e G+GF+ + rGs++nD + + ++ ++ lcl|FitnessBrowser__Pedo557:CA265_RS11645 213 IGCVVKGCPAGLGEPVFDKLHADLGKAMLSINAVHGFEYGSGFAGSELRGSQHNDIPQPKaadSKVFK 280 *******************************************************4433222367789 PP TIGR00033 268 rktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravpvvEam 335 + tn GGi+GGi+nG+di++++a+Kp++ti ++++t++ +++ + kgRhDpcvvprav++vEam lcl|FitnessBrowser__Pedo557:CA265_RS11645 281 TTTNYAGGILGGISNGMDITFKVAFKPVATIMHNQQTINAAGEASEIKGKGRHDPCVVPRAVVIVEAM 348 999************************************9766555555******************* PP TIGR00033 336 valvladallekra 349 alvlad++l+++a lcl|FitnessBrowser__Pedo557:CA265_RS11645 349 AALVLADQFLRNKA 362 **********9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.49 // [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