Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_092998655.1 BLP65_RS14490 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_900102855.1:WP_092998655.1 Length = 362 Score = 426 bits (1096), Expect = e-124 Identities = 208/358 (58%), Positives = 267/358 (74%), Gaps = 5/358 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 + VDLG RSYPIYIG LL +P+L+ H+ G +V+VVTN TV PLYL+KT+ A Sbjct: 4 LHVDLGERSYPIYIGTDLLGRPELVSPHVRGSQVMVVTNETVGPLYLEKTLQAFAAFETG 63 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 V+LPDGEQ+K +ET ++FD +E R DRRCT VALGGGV+GD+ G+AAA Y RG Sbjct: 64 ----HVVLPDGEQYKTLETWNRIFDALLERRFDRRCTLVALGGGVVGDITGFAAACYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 V+FIQIPTT+++QVDSSVGGKTG+NHPLGKNMIGAF+QP+CVL DT TL TL R+LA+G Sbjct: 120 VDFIQIPTTLLSQVDSSVGGKTGVNHPLGKNMIGAFHQPRCVLADTATLQTLDSRQLAAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 +AEVIKYGLI D EF W E++M L RDP A +AI+RSC +KA VV++DE+E+G RA Sbjct: 180 IAEVIKYGLINDPEFLAWLEEHMAALTGRDPQALAFAIERSCADKAVVVAKDEREAGSRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 LNLGHTFGHA+ETG+GYG+WLHGEAVA G V+A ++S RLGWI + V+R + ++ +A Sbjct: 240 LLNLGHTFGHAIETGMGYGRWLHGEAVATGMVLAAELSERLGWIGSADVERARALIARAG 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438 LP P ++ + F +MAVDKKV GKLRL+L++G LG V T +D + + A Sbjct: 300 LPVQAPAELSADRFLELMAVDKKVIGGKLRLVLMEG-LGQSVVTDRFDPADIRAVIEA 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: 398 Number of extensions: 12 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: 362 Length adjustment: 31 Effective length of query: 411 Effective length of database: 331 Effective search space: 136041 Effective search space used: 136041 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 WP_092998655.1 BLP65_RS14490 (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.14816.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-119 383.1 0.0 6.9e-119 383.0 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092998655.1 BLP65_RS14490 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092998655.1 BLP65_RS14490 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.0 0.0 6.9e-119 6.9e-119 1 338 [. 13 349 .. 13 355 .. 0.94 Alignments for each domain: == domain 1 score: 383.0 bits; conditional E-value: 6.9e-119 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g++ll + e ++ + s+++v+t+e+v l+ ek ++a ++ +e+ ++v+pdge++K+let lcl|NCBI__GCF_900102855.1:WP_092998655.1 13 YPIYIGTDLLGRP-ELVSPhvRGSQVMVVTNETVGPLYLEKTLQAFAA--FETGHVVLPDGEQYKTLET 78 5678888888743.3333333569**************8888888765..9****************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +++ d+lle+ ++r+ +lva+GGGvvgD++GF+Aa y+RG++++q+PTtll++vDssvGGKtg+n+pl lcl|NCBI__GCF_900102855.1:WP_092998655.1 79 WNRIFDALLERRFDRRCTLVALGGGVVGDITGFAAACYQRGVDFIQIPTTLLSQVDSSVGGKTGVNHPL 147 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGaf+qP+ Vl d+++l+tl++r+l++G+aEviK+gli+d e++++le++ ++l+ + + +al+ lcl|NCBI__GCF_900102855.1:WP_092998655.1 148 GKNMIGAFHQPRCVLADTATLQTLDSRQLAAGIAEVIKYGLINDPEFLAWLEEHMAALTGR-DPQALAF 215 ********************************************************99986.55***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+rs+ Ka vV++De+e+g RalLN+GHt+gHaiE+ ++y+ + HGeaVa+Gmv++a+lse+lg + lcl|NCBI__GCF_900102855.1:WP_092998655.1 216 AIERSCADKAVVVAKDEREAGSRALLNLGHTFGHAIETGMGYGrWLHGEAVATGMVLAAELSERLGWIG 284 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteee 338 + ++er +al+ ++glp++ + +ls++ +l+ + DKK g+k++lvl+e +G+ +++++++ + lcl|NCBI__GCF_900102855.1:WP_092998655.1 285 SADVERARALIARAGLPVQAPAELSADRFLELMAVDKKVIGGKLRLVLMEGLGQSVVTDRFDPAD 349 *******************************************************9998875554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (362 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: 9.64 // [ok]
This GapMind analysis is from Apr 10 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