Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF3646 Psest_3713 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >FitnessBrowser__psRCH2:GFF3646 Length = 367 Score = 428 bits (1100), Expect = e-124 Identities = 221/358 (61%), Positives = 269/358 (75%), Gaps = 5/358 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 ++VDLG RSYPI+IG LLD+P+L I G++V +VTN TVAPLYLD+ L+ N Sbjct: 4 LQVDLGERSYPIHIGERLLDRPELFSDKIRGRQVAIVTNETVAPLYLDRLTRTLS----N 59 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 V VILPDGE+ KN +TL +FD + +R DR T +ALGGGV+GDM GYAAASY RG Sbjct: 60 HAVTPVILPDGEEHKNWQTLQLIFDALLGARHDRNTTIIALGGGVVGDMAGYAAASYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNMIGAFYQP+ V+IDT TL TLP REL++G Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPRAVVIDTTTLATLPARELSAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 LAEVIKYGLI D F W E N+ L+ A D A T AI+RSC KA VV+ DE+ESGVRA Sbjct: 180 LAEVIKYGLICDEPFLGWLETNIDLIRALDSAALTEAIQRSCAAKAKVVNADERESGVRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 LNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS +LGWI ++ R ++LQ+A Sbjct: 240 ILNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSCQLGWIGEAERDRAIRLLQRAA 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438 LP PP M + F MAVDKKV DG+LRL+LL+ LG V TGD+ + L+ TL A Sbjct: 300 LPVVPPAQMRPQDFLEHMAVDKKVLDGRLRLVLLR-QLGEAVVTGDFPRDVLETTLNA 356 Lambda K H 0.318 0.133 0.385 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: 430 Number of extensions: 7 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: 367 Length adjustment: 31 Effective length of query: 411 Effective length of database: 336 Effective search space: 138096 Effective search space used: 138096 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 GFF3646 Psest_3713 (3-dehydroquinate synthase)
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.18724.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-119 385.4 0.0 1.4e-119 385.2 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3646 Psest_3713 3-dehydroquinate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3646 Psest_3713 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 385.2 0.0 1.4e-119 1.4e-119 1 339 [. 13 350 .. 13 355 .. 0.95 Alignments for each domain: == domain 1 score: 385.2 bits; conditional E-value: 1.4e-119 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldq 74 y++++ge ll++ ++ + +++ ++t+e+v+ l+ ++l ++l++ +v+ +++pdgee+K+++t++ + d+ lcl|FitnessBrowser__psRCH2:GFF3646 13 YPIHIGERLLDRPELFSDKiRGRQVAIVTNETVAPLYLDRLTRTLSN--HAVTPVILPDGEEHKNWQTLQLIFDA 85 68999999999553333344569**********************87..9999********************** PP TIGR01357 75 lleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPka 149 ll + ++r+++++a+GGGvvgD+aG++Aa+y+RG++++qvPTtll++vDssvGGKtgin+plgkN+iGafyqP+a lcl|FitnessBrowser__psRCH2:GFF3646 86 LLGARHDRNTTIIALGGGVVGDMAGYAAASYQRGVDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPRA 160 *************************************************************************** PP TIGR01357 150 VlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDeke 224 V+id+++l+tlp rel++G+aEviK+gli d+ ++ +le+n +l++ l + +al+e+i+rs+ Ka+vV++De+e lcl|FitnessBrowser__psRCH2:GFF3646 161 VVIDTTTLATLPARELSAGLAEVIKYGLICDEPFLGWLETNIDLIRAL-DSAALTEAIQRSCAAKAKVVNADERE 234 *******************************************88876.55************************ PP TIGR01357 225 sglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkkls 298 sg+Ra+LN+GHt+gHaiE+ ++y+ + HGeaVa G v+++++s +lg + + +++r ++ll+++ lp+ + +++ lcl|FitnessBrowser__psRCH2:GFF3646 235 SGVRAILNLGHTFGHAIETHMGYGvWLHGEAVAAGTVMALEMSCQLGWIGEAERDRAIRLLQRAALPVVPPAQMR 309 *************************************************************************** PP TIGR01357 299 veellkallkDKKnegskiklvlleeiGkaalasevteeel 339 + +l+++ DKK +++++lvll+++G+a+++ +++++ l lcl|FitnessBrowser__psRCH2:GFF3646 310 PQDFLEHMAVDKKVLDGRLRLVLLRQLGEAVVTGDFPRDVL 350 ******************************99988876654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (367 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: 10.49 // [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