Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_086509303.1 BZY95_RS07350 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_002151265.1:WP_086509303.1 Length = 370 Score = 391 bits (1004), Expect = e-113 Identities = 201/368 (54%), Positives = 259/368 (70%), Gaps = 4/368 (1%) Query: 74 SSQAPTVVEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISA 133 +S P ++V LG RSYPI+IGAGLL P L ++ G++V++VTN VAP YL++ + Sbjct: 6 TSIVPRTLQVALGERSYPIHIGAGLLGDPAWLTPYLAGRQVMIVTNEAVAPHYLERLKAG 65 Query: 134 LTDGNPNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYA 193 L + V ++LPDGE K + ++ V+D +E+ +RRCT +ALGGGVIGDM G+A Sbjct: 66 LPS---DAVVRELVLPDGEATKTLASVGLVWDALLEAGFNRRCTLIALGGGVIGDMVGFA 122 Query: 194 AASYLRGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLP 253 AA Y RGV FIQ+PTT+++QVDSSVGGKTG+NHPLGKNMIGAF+QP+ VLIDTDTL TLP Sbjct: 123 AACYQRGVAFIQVPTTLLSQVDSSVGGKTGVNHPLGKNMIGAFWQPRAVLIDTDTLRTLP 182 Query: 254 DRELASGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDE 313 +EL++GLAEVIKYGLIRDAEF W E M L A A +AI+RSC KA++V++DE Sbjct: 183 AKELSAGLAEVIKYGLIRDAEFLAWLEDEMTALRALQSEALAWAIERSCRLKAEIVAEDE 242 Query: 314 KESGVRATLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQ 373 E GVRA LNLGHTFGHA+E GYGQWLHGEAV G +MA ++S RLGW++ V+R Sbjct: 243 TEQGVRALLNLGHTFGHAIEAHQGYGQWLHGEAVGVGMLMAAELSHRLGWLNAGDVERTA 302 Query: 374 KILQQAKLPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALD 433 I+ A LP P M VE F + M +DKK D +LRLILL+ +LG V ++ L+ Sbjct: 303 SIIAAAGLPLEAPADMGVEDFLTRMRLDKKNVDERLRLILLE-ALGRAVIHDQTPRELLE 361 Query: 434 ETLRAFSK 441 E L F + Sbjct: 362 ELLATFPR 369 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: 392 Number of extensions: 11 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: 370 Length adjustment: 31 Effective length of query: 411 Effective length of database: 339 Effective search space: 139329 Effective search space used: 139329 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_086509303.1 BZY95_RS07350 (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.4015.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-121 389.9 0.0 6.1e-121 389.8 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509303.1 BZY95_RS07350 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509303.1 BZY95_RS07350 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.8 0.0 6.1e-121 6.1e-121 1 339 [. 22 360 .. 22 365 .. 0.95 Alignments for each domain: == domain 1 score: 389.8 bits; conditional E-value: 6.1e-121 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 y++++g gll + + ++++++t+e+v+ ++ e+l++ l s + v +lv+pdge +K+l++v lcl|NCBI__GCF_002151265.1:WP_086509303.1 22 YPIHIGAGLLGDPAWLTPYlAGRQVMIVTNEAVAPHYLERLKAGLPS-DAVVRELVLPDGEATKTLASV 89 578888888885543333334599*********************98.9999***************** PP TIGR01357 69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137 ++d+lle++++r+ +l+a+GGGv+gD++GF+Aa y+RG++++qvPTtll++vDssvGGKtg+n+plg lcl|NCBI__GCF_002151265.1:WP_086509303.1 90 GLVWDALLEAGFNRRCTLIALGGGVIGDMVGFAAACYQRGVAFIQVPTTLLSQVDSSVGGKTGVNHPLG 158 ********************************************************************* PP TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206 kN+iGaf+qP+aVlid+++l+tlp +el++G+aEviK+gli dae++++le+ +l+ l + eal+ + lcl|NCBI__GCF_002151265.1:WP_086509303.1 159 KNMIGAFWQPRAVLIDTDTLRTLPAKELSAGLAEVIKYGLIRDAEFLAWLEDEMTALRAL-QSEALAWA 226 ****************************************************99988876.55****** PP TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274 i+rs+++Kae+V+eDe+e+g+RalLN+GHt+gHaiEa +y+ + HGeaV +Gm ++a+ls++lg l+a lcl|NCBI__GCF_002151265.1:WP_086509303.1 227 IERSCRLKAEIVAEDETEQGVRALLNLGHTFGHAIEAHQGYGqWLHGEAVGVGMLMAAELSHRLGWLNA 295 *****************************************99************************** PP TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339 ++er+++++ ++glp + + ++ ve +l + DKKn +++++l+lle++G+a++++++++e l lcl|NCBI__GCF_002151265.1:WP_086509303.1 296 GDVERTASIIAAAGLPLEAPADMGVEDFLTRMRLDKKNVDERLRLILLEALGRAVIHDQTPRELL 360 *********************************************************77765544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (370 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: 11.52 // [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