Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_005810889.1 DHAF_RS17625 3-dehydroquinate synthase
Query= curated2:A4J3A3 (359 letters) >NCBI__GCF_000021925.1:WP_005810889.1 Length = 360 Score = 263 bits (672), Expect = 5e-75 Identities = 141/345 (40%), Positives = 214/345 (62%), Gaps = 5/345 (1%) Query: 11 RSYPIYIASAILDKIGTYLSEQ-PLGKKVLLVTDQQVAPLYAPRVIESLKNAGFKVAVAE 69 + YP+++ A L+++G YL+ + G+ +L++T V Y + + L + F V Sbjct: 12 KPYPVFLG-ARLEELGDYLTTRIGAGEHLLVITHPNVGDYYLDTLQKGLSS--FMVNTLI 68 Query: 70 IPAGEPSKTLEQASRLYDLAFDHALDRQSSVIALGGGVVGDLAGFVAATYMRGVPFIQIP 129 +P GE K+L++ S L A DR++ V+ALGGGV+GDLAGF A+ +MRG+ ++QIP Sbjct: 69 VPQGEDEKSLDRLSDLTSEAIACGADRKTVVLALGGGVIGDLAGFFASVFMRGMRYVQIP 128 Query: 130 TTLLAQVDSSVGGKVAVNHSRGKNMIGAFYQPQMVMIDVATLQTLPERELKAGLAEVIKY 189 TTLLA VDSS+GGKVAVNH+ GKN++G FY P V D +TL+TLP E+ GLAE IK+ Sbjct: 129 TTLLAMVDSSIGGKVAVNHAAGKNLLGDFYPPLAVWTDFSTLETLPWEEMLNGLAETIKH 188 Query: 190 GVIWDGSFFTWLEKNYSRILNLDTTALEQVAETCCKIKASVVEQDEREQGCRAILNYGHT 249 VI D +++EK+ I+ +++ +K +V +DE EQG R LNYGH+ Sbjct: 189 AVIADEELLSFIEKHQEEIMARKPELYKELTSRSSAVKVRLVSEDETEQGKRMFLNYGHS 248 Query: 250 VGHAIESLSGYGTYLHGEAVAMGMISAARLALNEGILSQQDFERIYRLISAVGLPTELPR 309 GHA+E+ Y HG+ V++GM++AA LA G+++ + ER+ +L+ A GLP + R Sbjct: 249 FGHALEAEVAYQGITHGQGVSIGMVAAAHLAQERGLMNSGEVERLIKLLKAFGLPVTV-R 307 Query: 310 GLGPQDIIDSMYHDKKTVLGKLVFVLPRSLGQVDIFKDVKEADIL 354 P+ + D M DKK G+ V VLP+ +GQ + +D + +IL Sbjct: 308 AKNPRVLTDLMGADKKNYKGQKVLVLPKGIGQGIVIRDANDEEIL 352 Lambda K H 0.319 0.137 0.389 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: 296 Number of extensions: 10 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: 359 Length of database: 360 Length adjustment: 29 Effective length of query: 330 Effective length of database: 331 Effective search space: 109230 Effective search space used: 109230 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 WP_005810889.1 DHAF_RS17625 (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.29998.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-110 353.1 0.0 9.9e-110 352.9 0.0 1.0 1 lcl|NCBI__GCF_000021925.1:WP_005810889.1 DHAF_RS17625 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_005810889.1 DHAF_RS17625 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.9 0.0 9.9e-110 9.9e-110 20 342 .. 35 354 .. 15 356 .. 0.95 Alignments for each domain: == domain 1 score: 352.9 bits; conditional E-value: 9.9e-110 TIGR01357 20 kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleeklerksvlva 88 ++l+vit+ +v +++ ++l++ l+s + v +l+vp+ge Ksl+++++l+++ ++ +++rk+v++a lcl|NCBI__GCF_000021925.1:WP_005810889.1 35 AGEHLLVITHPNVGDYYLDTLQKGLSS--FMVNTLIVPQGEDEKSLDRLSDLTSEAIACGADRKTVVLA 101 35899********************87..99************************************** PP TIGR01357 89 iGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlkvl 157 +GGGv+gDlaGF A++++RG+r+vq+PTtllamvDss+GGK+++n++ gkNl+G fy P aV++d ++l lcl|NCBI__GCF_000021925.1:WP_005810889.1 102 LGGGVIGDLAGFFASVFMRGMRYVQIPTTLLAMVDSSIGGKVAVNHAAGKNLLGDFYPPLAVWTDFSTL 170 ********************************************************************* PP TIGR01357 158 etlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesg 226 etlp +e+ +G+aE iKh++iad+el++++ek+++++ + + e +el +rs vK ++V+eDe+e+g lcl|NCBI__GCF_000021925.1:WP_005810889.1 171 ETLPWEEMLNGLAETIKHAVIADEELLSFIEKHQEEIMAR-KPELYKELTSRSSAVKVRLVSEDETEQG 238 ***********************************98875.569************************* PP TIGR01357 227 lRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklk 294 R++LN+GH++gHa+Ea++ y+ ++HG+ V+iGmv +a+l+++ gl+++ ++erl++llk++glp++++ lcl|NCBI__GCF_000021925.1:WP_005810889.1 239 KRMFLNYGHSFGHALEAEVAYQgITHGQGVSIGMVAAAHLAQERGLMNSGEVERLIKLLKAFGLPVTVR 307 ********************************************************************* PP TIGR01357 295 kklsveellkallkDKKnegskiklvlleeiGkaalasevteeellea 342 + l++ + DKKn ++++ lvl++ iG+ ++ ++ +ee+l+a lcl|NCBI__GCF_000021925.1:WP_005810889.1 308 A-KNPRVLTDLMGADKKNYKGQKVLVLPKGIGQGIVIRDANDEEILRA 354 7.999****************************999999999988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (360 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: 12.30 // [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