Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_077279834.1 B1C78_RS14160 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_002000365.1:WP_077279834.1 Length = 365 Score = 459 bits (1181), Expect = e-134 Identities = 222/354 (62%), Positives = 283/354 (79%), Gaps = 5/354 (1%) Query: 83 VDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPNVT 142 V+LG RSYPI+IG GLLD P HI G+RV++VTN TVAPLYLD+ + L+ Sbjct: 6 VELGERSYPIHIGRGLLDDPQRFAPHIRGQRVMIVTNETVAPLYLDRLKATLS----GFL 61 Query: 143 VESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRGVN 202 V++VILPDGE++KN+ETL +++ +E R DRR T VALGGGV+GD+ G+AAASY RGV+ Sbjct: 62 VDTVILPDGEEYKNLETLNRIYTALLEGRFDRRSTLVALGGGVVGDITGFAAASYQRGVD 121 Query: 203 FIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASGLA 262 F+Q+PTT+++QVDSSVGGKTG+NHPLGKNMIGAF+QP+CV+IDTDTLNTLPDREL +G+A Sbjct: 122 FLQVPTTLLSQVDSSVGGKTGVNHPLGKNMIGAFHQPRCVVIDTDTLNTLPDRELHAGIA 181 Query: 263 EVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRATL 322 EVIKYGLI D FFEW E++M LLAR+P YAI RSC++KA VV++DE+ESG RA L Sbjct: 182 EVIKYGLICDRPFFEWLEEHMEGLLAREPGTLAYAIHRSCQDKAQVVAEDERESGRRAIL 241 Query: 323 NLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAKLP 382 NLGHTFGHA+ETG+GYG WLHGE VAAG VMA MSRRLGWIDD + R + +++ A LP Sbjct: 242 NLGHTFGHAIETGMGYGVWLHGEGVAAGMVMAARMSRRLGWIDDGELTRTEALVRAAGLP 301 Query: 383 TSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436 +PP ++ + F +M+VDKKV DG+LRL+LL+G +G V T ++D +AL+ETL Sbjct: 302 CAPPPELSPDRFMQLMSVDKKVLDGQLRLVLLRG-IGEAVVTAEFDPRALEETL 354 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: 447 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: 365 Length adjustment: 31 Effective length of query: 411 Effective length of database: 334 Effective search space: 137274 Effective search space used: 137274 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_077279834.1 B1C78_RS14160 (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.2579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-122 394.5 0.0 2.5e-122 394.3 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077279834.1 B1C78_RS14160 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077279834.1 B1C78_RS14160 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 394.3 0.0 2.5e-122 2.5e-122 1 341 [. 13 352 .. 13 355 .. 0.96 Alignments for each domain: == domain 1 score: 394.3 bits; conditional E-value: 2.5e-122 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 y++++g+gll+ ++ + + ++++++t+e+v+ l+ ++l+++l+ g+ v+++++pdgee+K+let+ lcl|NCBI__GCF_002000365.1:WP_077279834.1 13 YPIHIGRGLLDDPQRFAPHiRGQRVMIVTNETVAPLYLDRLKATLS--GFLVDTVILPDGEEYKNLETL 79 689********887777776679*********************95..8******************** PP TIGR01357 69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137 ++++++lle ++r+s+lva+GGGvvgD++GF+Aa+y+RG+++ qvPTtll++vDssvGGKtg+n+plg lcl|NCBI__GCF_002000365.1:WP_077279834.1 80 NRIYTALLEGRFDRRSTLVALGGGVVGDITGFAAASYQRGVDFLQVPTTLLSQVDSSVGGKTGVNHPLG 148 ********************************************************************* PP TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206 kN+iGaf+qP+ V+id+++l+tlp+rel +G+aEviK+gli d+ +fe+le++ + ll + e +l+ + lcl|NCBI__GCF_002000365.1:WP_077279834.1 149 KNMIGAFHQPRCVVIDTDTLNTLPDRELHAGIAEVIKYGLICDRPFFEWLEEHMEGLLAR-EPGTLAYA 216 ******************************************************988875.6699**** PP TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274 i rs++ Ka+vV+eDe+esg Ra+LN+GHt+gHaiE+ ++y+ + HGe Va Gmv++a++s++lg ++ lcl|NCBI__GCF_002000365.1:WP_077279834.1 217 IHRSCQDKAQVVAEDERESGRRAILNLGHTFGHAIETGMGYGvWLHGEGVAAGMVMAARMSRRLGWIDD 285 ********************************************************************* PP TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341 +l r++al++++glp +++ls + +++ ++ DKK +++++lvll+ iG+a+++ e++ ++l e lcl|NCBI__GCF_002000365.1:WP_077279834.1 286 GELTRTEALVRAAGLPCAPPPELSPDRFMQLMSVDKKVLDGQLRLVLLRGIGEAVVTAEFDPRALEE 352 *******************************************************999997776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (365 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: 10.73 // [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