Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate Pf6N2E2_3754 3-dehydroquinate synthase (EC 4.2.3.4)
Query= SwissProt::Q8RU74 (442 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 Length = 366 Score = 439 bits (1129), Expect = e-128 Identities = 227/358 (63%), Positives = 273/358 (76%), Gaps = 5/358 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 ++VDLG RSYPI+IG GLLDQP+LL HI G++V +++N TVAPLYL++ +L+ Sbjct: 4 LKVDLGERSYPIHIGEGLLDQPELLAPHIAGRQVAIISNETVAPLYLERLTRSLSA---- 59 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 +V SV+LPDGE FKN ETL +FD + +R DRR T +ALGGGVIGDM G+AAA Y RG Sbjct: 60 FSVISVVLPDGEAFKNWETLQLIFDGLLTARHDRRTTVLALGGGVIGDMAGFAAACYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 V+FIQIPTT+++QVDSSVGGKTGINHPLGKNM+GAFYQP VLIDT TLNTLP REL++G Sbjct: 120 VDFIQIPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPNVVLIDTATLNTLPARELSAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 LAEVIKYGLI D F W E+N+ L A D A TYAI+RSC KA VV DE+ESGVRA Sbjct: 180 LAEVIKYGLICDEPFLGWLEENVDRLRALDQAALTYAIERSCAAKAAVVGADERESGVRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 TLNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS RLGWI + R ++ Q+A Sbjct: 240 TLNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSARLGWISEQERDRGIRLFQRAG 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438 LP PPE MT F MA+DKKV DG+LRL+LL+ +G V T DY ++ L TL A Sbjct: 300 LPVVPPEEMTEADFLEHMAIDKKVIDGRLRLVLLR-HMGEAVVTDDYPKEVLQATLGA 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: 425 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: 366 Length adjustment: 31 Effective length of query: 411 Effective length of database: 335 Effective search space: 137685 Effective search space used: 137685 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 Pf6N2E2_3754 (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.9656.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-119 382.8 0.0 9.9e-119 382.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 3-dehydroquinate synthase (EC 4. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 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 ! 382.5 0.0 9.9e-119 9.9e-119 1 340 [. 13 351 .. 13 354 .. 0.96 Alignments for each domain: == domain 1 score: 382.5 bits; conditional E-value: 9.9e-119 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesK 63 y++++gegll++ + +++ +i++e+v+ l+ e+l + l++ ++v+ +v+pdge K lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 13 YPIHIGEGLLDQPELLAPHiAGRQVAIISNETVAPLYLERLTRSLSA--FSVISVVLPDGEAFK 74 689********774444444459**********************76..*************** PP TIGR01357 64 sletvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvG 127 ++et++ + d ll++ ++r+++++a+GGGv+gD+aGF+Aa y+RG++++q+PTtll++vDssvG lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 75 NWETLQLIFDGLLTARHDRRTTVLALGGGVIGDMAGFAAACYQRGVDFIQIPTTLLSQVDSSVG 138 **************************************************************** PP TIGR01357 128 GKtginlplgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekne 191 GKtgin+plgkN++GafyqP++Vlid+++l+tlp rel++G+aEviK+gli d+ ++ +le+n lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 139 GKTGINHPLGKNMVGAFYQPNVVLIDTATLNTLPARELSAGLAEVIKYGLICDEPFLGWLEENV 202 **************************************************************** PP TIGR01357 192 klllklaelealeelikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGea 254 + l+ l +++al+ +i+rs+ Ka vV +De+esg+Ra+LN+GHt+gHaiE+ ++y+ + HGea lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 203 DRLRAL-DQAALTYAIERSCAAKAAVVGADERESGVRATLNLGHTFGHAIETHMGYGvWLHGEA 265 987765.66******************************************************* PP TIGR01357 255 VaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkDKKnegskik 318 Va G v+++++s +lg +++++++r ++l++++glp+ +++++ +l+++ DKK +++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 266 VAAGTVMALEMSARLGWISEQERDRGIRLFQRAGLPVVPPEEMTEADFLEHMAIDKKVIDGRLR 329 **************************************************************** PP TIGR01357 319 lvlleeiGkaalasevteeell 340 lvll+++G+a++++++++e l+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3754 330 LVLLRHMGEAVVTDDYPKEVLQ 351 ************9998777654 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.40 // [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