Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011938715.1 GURA_RS09230 3-dehydroquinate synthase
Query= BRENDA::Q3M4V2 (363 letters) >NCBI__GCF_000016745.1:WP_011938715.1 Length = 360 Score = 308 bits (788), Expect = 2e-88 Identities = 169/343 (49%), Positives = 226/343 (65%), Gaps = 3/343 (0%) Query: 5 INVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGF 64 I V L +SY I L +G A KLG++V +V+NPT+ + + +SL +AGF Sbjct: 4 ITVGLDERSYPIFFNVNELSMLGSLCADQKLGQRVAVVTNPTVGAWYFEPVRESLVSAGF 63 Query: 65 QVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGI 124 V +P GE YK ++++ +YD ++ L+R S +VALGGGVIGDM G+AAAT+LRGI Sbjct: 64 SVHKIEVPDGEEYKNSDTLKDIYDWLIDFGLDRGSFIVALGGGVIGDMAGYAAATYLRGI 123 Query: 125 NVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGM 184 VQVPTTLLA VDS++GGKTG+NH GKNLIGAF+QPR V+ID VL TL RE+ +G+ Sbjct: 124 PFVQVPTTLLAQVDSSVGGKTGINHEKGKNLIGAFYQPRLVMIDVAVLDTLAEREYLSGL 183 Query: 185 AEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKEGGLR 244 AE+ KYGV+ DAE F + + +++L E + A + RSC KA VV +DE+EGGLR Sbjct: 184 AEMAKYGVVLDAEFFRFMYDN--VEKLLSRDKECLLAAVKRSCALKASVVEQDEREGGLR 241 Query: 245 AILNYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEKA 304 A+LNYGHT+GHAVE+LT YR HGEAV IGM A +I+ ++G D +R +L+ K Sbjct: 242 AVLNYGHTIGHAVETLTGYRQYLHGEAVAIGMAQAAKISESMGFSSSDDTERVLSLLSKL 301 Query: 305 GLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTV 347 LP LP E IEA+ DKKV+DG + FV +G T+ Sbjct: 302 KLPQDLPPFSPSE-YIEAICHDKKVRDGGLNFVFNKNLGSFTI 343 Lambda K H 0.319 0.136 0.388 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: 317 Number of extensions: 16 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: 363 Length of database: 360 Length adjustment: 29 Effective length of query: 334 Effective length of database: 331 Effective search space: 110554 Effective search space used: 110554 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_011938715.1 GURA_RS09230 (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.3444.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-120 387.9 0.0 2.4e-120 387.8 0.0 1.0 1 lcl|NCBI__GCF_000016745.1:WP_011938715.1 GURA_RS09230 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016745.1:WP_011938715.1 GURA_RS09230 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.8 0.0 2.4e-120 2.4e-120 18 334 .. 30 346 .. 13 356 .. 0.94 Alignments for each domain: == domain 1 score: 387.8 bits; conditional E-value: 2.4e-120 TIGR01357 18 aeka..sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleeklerks 84 a+++ +++ v+t+ +v + + e ++e l s+g++v+++ vpdgee+K+ +t+++++d+l++ +l+r s lcl|NCBI__GCF_000016745.1:WP_011938715.1 30 ADQKlgQRVAVVTNPTVGAWYFEPVRESLVSAGFSVHKIEVPDGEEYKNSDTLKDIYDWLIDFGLDRGS 98 43223489************************************************************* PP TIGR01357 85 vlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlid 153 +va+GGGv+gD+aG++AatylRGi++vqvPTtlla+vDssvGGKtgin+++gkNliGafyqP++V+id lcl|NCBI__GCF_000016745.1:WP_011938715.1 99 FIVALGGGVIGDMAGYAAATYLRGIPFVQVPTTLLAQVDSSVGGKTGINHEKGKNLIGAFYQPRLVMID 167 ********************************************************************* PP TIGR01357 154 lkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDe 222 ++vl tl+ere+ +G+aE+ K+g++ dae+f+++ +n ++ll++++ e l ++krs+ +Ka+vVe+De lcl|NCBI__GCF_000016745.1:WP_011938715.1 168 VAVLDTLAEREYLSGLAEMAKYGVVLDAEFFRFMYDNVEKLLSRDK-ECLLAAVKRSCALKASVVEQDE 235 *************************************999997655.********************** PP TIGR01357 223 kesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglp 290 +e glRa+LN+GHt+gHa+E+l++y+ + HGeaVaiGm+++ak+se++g+ +++++er+++ll+kl+lp lcl|NCBI__GCF_000016745.1:WP_011938715.1 236 REGGLRAVLNYGHTIGHAVETLTGYRqYLHGEAVAIGMAQAAKISESMGFSSSDDTERVLSLLSKLKLP 304 **************************9****************************************** PP TIGR01357 291 tklkkklsveellkallkDKKnegskiklvlleeiGkaalasev 334 ++l++ +s +e+++a+ +DKK +++ +++v+ +++G+ ++a+ v lcl|NCBI__GCF_000016745.1:WP_011938715.1 305 QDLPP-FSPSEYIEAICHDKKVRDGGLNFVFNKNLGSFTIAT-V 346 ****7.********************************9994.4 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: 6.96 // [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