Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate Dsui_1095 Dsui_1095 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >FitnessBrowser__PS:Dsui_1095 Length = 364 Score = 402 bits (1032), Expect = e-116 Identities = 208/358 (58%), Positives = 268/358 (74%), Gaps = 8/358 (2%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 ++V LG RSYPI+IG+GLL + DL+ H+ K+ ++V+N TVAPLYL+ ++AL N Sbjct: 6 LQVALGDRSYPIHIGSGLLQRADLILPHLGRKKAVIVSNETVAPLYLEP-LAALLRAN-G 63 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 V V V+LPDGE+FK+ TL ++FD +ESR +R T +ALGGGVIGD G+AAA Y RG Sbjct: 64 VAVSQVVLPDGEEFKDWPTLNRIFDALLESRAERSTTLIALGGGVIGDTTGFAAACYQRG 123 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 + FIQ+PTT+++QVDSSVGGKT INHPLGKNMIGAFYQP+ VL D DTL+TLP+REL +G Sbjct: 124 MPFIQVPTTLLSQVDSSVGGKTAINHPLGKNMIGAFYQPKLVLADIDTLDTLPERELKAG 183 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 LAEVIKYGLIRD +F W E ++P LLARD A+ RSC +KA+VV++DE+E+G RA Sbjct: 184 LAEVIKYGLIRDPQFLGWIESSLPGLLARDKALLAEAVYRSCAHKAEVVARDERETGERA 243 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 LNLGHTFGHA+ETG+GYG WLHGEAVAAGTVMA ++S RLGWI + V RV+ + + A Sbjct: 244 LLNLGHTFGHAIETGLGYGVWLHGEAVAAGTVMAAELSARLGWIGPAEVARVESVFRLAG 303 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438 LP S P+ + VE + +M DKKV GKLRL+L +G +G+ V + A DE + A Sbjct: 304 LPVSGPD-LGVERYLELMRHDKKVEAGKLRLVLFRG-IGDAVVS----DAASDEQIAA 355 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: 401 Number of extensions: 9 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: 442 Length of database: 364 Length adjustment: 31 Effective length of query: 411 Effective length of database: 333 Effective search space: 136863 Effective search space used: 136863 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 Dsui_1095 Dsui_1095 (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.13434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-118 381.8 0.0 1.8e-118 381.6 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_1095 Dsui_1095 3-dehydroquinate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_1095 Dsui_1095 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.6 0.0 1.8e-118 1.8e-118 1 340 [. 15 354 .. 15 358 .. 0.96 Alignments for each domain: == domain 1 score: 381.6 bits; conditional E-value: 1.8e-118 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqll 76 y++++g+gll+++ l + ++k+v++++e+v+ l+ e l+++l+++gv+v ++v+pdgee K++ t++++ d+ll lcl|FitnessBrowser__PS:Dsui_1095 15 YPIHIGSGLLQRADLILPHlGRKKAVIVSNETVAPLYLEPLAALLRANGVAVSQVVLPDGEEFKDWPTLNRIFDALL 91 689*******98877777755599***************************************************** PP TIGR01357 77 eeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlid 153 e+ +er+++l+a+GGGv+gD +GF+Aa y+RG++++qvPTtll++vDssvGGKt+in+plgkN+iGafyqPk+Vl d lcl|FitnessBrowser__PS:Dsui_1095 92 ESRAERSTTLIALGGGVIGDTTGFAAACYQRGMPFIQVPTTLLSQVDSSVGGKTAINHPLGKNMIGAFYQPKLVLAD 168 ***************************************************************************** PP TIGR01357 154 lkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRal 230 +++l tlperel++G+aEviK+gli d +++ ++e+ ll + +++ l+e++ rs+ KaevV++De+e+g Ral lcl|FitnessBrowser__PS:Dsui_1095 169 IDTLDTLPERELKAGLAEVIKYGLIRDPQFLGWIESSLPGLLAR-DKALLAEAVYRSCAHKAEVVARDERETGERAL 244 ************************************99988876.55****************************** PP TIGR01357 231 LNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkal 306 LN+GHt+gHaiE+ l+y+ + HGeaVa G v++a+ls +lg + + ++ r++++++ +glp++ ++ l ve +l+ + lcl|FitnessBrowser__PS:Dsui_1095 245 LNLGHTFGHAIETGLGYGvWLHGEAVAAGTVMAAELSARLGWIGPAEVARVESVFRLAGLPVSGPD-LGVERYLELM 320 *****************************************************************7.********** PP TIGR01357 307 lkDKKnegskiklvlleeiGkaalasevteeell 340 +DKK e++k++lvl + iG+a++++ ++e++ lcl|FitnessBrowser__PS:Dsui_1095 321 RHDKKVEAGKLRLVLFRGIGDAVVSDAASDEQIA 354 ************************9877777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (364 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: 9.25 // [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