Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate Ga0059261_3591 Ga0059261_3591 3-dehydroquinate synthase (EC 4.2.3.4)
Query= BRENDA::P07639 (362 letters) >FitnessBrowser__Korea:Ga0059261_3591 Length = 366 Score = 273 bits (697), Expect = 7e-78 Identities = 161/345 (46%), Positives = 212/345 (61%), Gaps = 7/345 (2%) Query: 1 MERIVVTLGERSYPITIASGLFNEPASFL-PLKSGEQVMLVTNETLAPLYLDKVRGVLEQ 59 M + V LG RSY + I SGL A L P ++VT+ +AP + +++ L Sbjct: 1 MRTVPVALGARSYEVRIESGLLGRAAEQLAPFVRKRPFVIVTDANVAP-HGERLAANLAA 59 Query: 60 AGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQ 119 AG+ +++ILP GE KS L+++ LL R ++ALGGGV+GDL GFA+A + Sbjct: 60 AGIASETIILPPGEGTKSWTQLESLLDRLLDLGIERGDHVIALGGGVIGDLVGFASAILK 119 Query: 120 RGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELA 179 RG F+Q+PTTLL+QVDSSVGGKTA+N GKN++GAF+QP+ V++D D L TLP RE Sbjct: 120 RGCNFVQIPTTLLAQVDSSVGGKTAINARAGKNLVGAFHQPSVVLIDPDLLDTLPLREQR 179 Query: 180 SGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERE-TG 238 +G AEV+KYG+I D FF W E N ALL D A Y I KA +VA DERE TG Sbjct: 180 AGYAEVVKYGLIDDADFFAWCEGNGAALLAGDPNAREYAIAHSVGAKARIVADDERETTG 239 Query: 239 LRALLNLGHTFGHAIEAEMGYGN-WLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLL 297 RALLNLGHTFGHA+EAE G+ + LHGE VAAGM +A S R G + + +R+ L Sbjct: 240 RRALLNLGHTFGHALEAETGFSDQLLHGEGVAAGMALAFAFSARQGLCPATDAERVAAHL 299 Query: 298 KRAGLP---VNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIG 339 K +GLP + + + HML DKK+ AG + +L IG Sbjct: 300 KASGLPHDLASAGIATNGARLVEHMLHDKKMDAGTLPFLLTRGIG 344 Lambda K H 0.320 0.136 0.392 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: 312 Number of extensions: 12 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: 362 Length of database: 366 Length adjustment: 29 Effective length of query: 333 Effective length of database: 337 Effective search space: 112221 Effective search space used: 112221 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate Ga0059261_3591 Ga0059261_3591 (3-dehydroquinate synthase (EC 4.2.3.4))
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))
# 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/TIGR01357.hmm # target sequence database: /tmp/gapView.20222.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01357 [M=344] Accession: TIGR01357 Description: aroB: 3-dehydroquinate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-108 348.2 0.0 3e-108 348.0 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3591 Ga0059261_3591 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_3591 Ga0059261_3591 3-dehydroquinate synthase (EC 4.2.3.4) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.0 0.0 3e-108 3e-108 1 338 [. 13 356 .. 13 362 .. 0.95 Alignments for each domain: == domain 1 score: 348.0 bits; conditional E-value: 3e-108 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y+v +++gll +++e+la +++ v++td +v+ ++e+l++ l+++g++ +++++p+ge +Ks+++ lcl|FitnessBrowser__Korea:Ga0059261_3591 13 YEVRIESGLLGRAAEQLAPfvRKRPFVIVTDANVAP-HGERLAANLAAAGIASETIILPPGEGTKSWTQ 80 6899**************986667888888888887.779999999999******************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +++lld+ll+ ++er + ++a+GGGv+gDl+GF+ a+ +RG ++vq+PTtlla+vDssvGGKt+in + lcl|FitnessBrowser__Korea:Ga0059261_3591 81 LESLLDRLLDLGIERGDHVIALGGGVIGDLVGFASAILKRGCNFVQIPTTLLAQVDSSVGGKTAINARA 149 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNl+Gaf+qP++Vlid+++l tlp re r+G+aEv+K+gli da++f+++e n ++ll + +a e lcl|FitnessBrowser__Korea:Ga0059261_3591 150 GKNLVGAFHQPSVVLIDPDLLDTLPLREQRAGYAEVVKYGLIDDADFFAWCEGNGAALLAG-DPNAREY 217 *******************************************************999875.55999** PP TIGR01357 206 likrsievKaevVeeDekes.glRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271 +i++s+ Ka++V+ De+e+ g RalLN+GHt+gHa+Ea+++++ l HGe Va Gm++++ +s + gl lcl|FitnessBrowser__Korea:Ga0059261_3591 218 AIAHSVGAKARIVADDERETtGRRALLNLGHTFGHALEAETGFSdqLLHGEGVAAGMALAFAFSARQGL 286 *******************99********************99889*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk...klsveellkallkDKKnegskiklvlleeiGkaalasevtee 337 ++a+++er++a lk+ glp +l + ++ l++++l+DKK++++++ + l + iG ++l+++v lcl|FitnessBrowser__Korea:Ga0059261_3591 287 CPATDAERVAAHLKASGLPHDLASagiATNGARLVEHMLHDKKMDAGTLPFLLTRGIGATYLDKQVNLA 355 ************************99889999******************************9888554 PP TIGR01357 338 e 338 + lcl|FitnessBrowser__Korea:Ga0059261_3591 356 D 356 4 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (366 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.43 // [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