Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_046061205.1 MEALZ_RS15785 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000968535.2:WP_046061205.1 Length = 361 Score = 425 bits (1092), Expect = e-123 Identities = 207/361 (57%), Positives = 269/361 (74%), Gaps = 5/361 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 ++VDLG RSYPIYIG+ LL++ DLL RHI K++L+VTN TVAPLYL + + L+D Sbjct: 4 LQVDLGQRSYPIYIGSRLLEKADLLTRHIRSKQILIVTNETVAPLYLQQVLDNLSD---- 59 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 VE+V+LPDGEQ+K ++ L ++FD + + R + +ALGGGVIGDM G+AAA Y RG Sbjct: 60 FVVETVVLPDGEQYKTLDYLNRIFDTLLAHKFSRNASLIALGGGVIGDMGGFAAACYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 + FIQIPTT++AQVDSSVGGKTG+NH LGKNMIGAFYQPQCV+ D L+TL DR+L++G Sbjct: 120 IPFIQIPTTLLAQVDSSVGGKTGVNHSLGKNMIGAFYQPQCVIADMSVLSTLDDRQLSAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 +AEVIKYGLIRD +FF W E N+ LL RD A +A++RSC NKA+VV+ DEKE+ VRA Sbjct: 180 IAEVIKYGLIRDPDFFSWLENNLESLLDRDAEALAHAVERSCRNKAEVVAADEKEADVRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 TLNLGHTFGHA+ETG+GYG +LHGEAVA GT A D+SRR GW+ D+ V+R+ ++ ++A+ Sbjct: 240 TLNLGHTFGHAIETGMGYGSYLHGEAVAIGTCQAADLSRRKGWLTDADVERIIRLFKRAR 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRAFS 440 LP PP + F +MAVDKK DG +RLILLK S+G ++ L TL + Sbjct: 300 LPVEPPVALDANRFIELMAVDKKNVDGNIRLILLK-SIGEATLPVGVEKALLVATLNGYG 358 Query: 441 K 441 + Sbjct: 359 R 359 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: 433 Number of extensions: 15 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: 361 Length adjustment: 31 Effective length of query: 411 Effective length of database: 330 Effective search space: 135630 Effective search space used: 135630 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_046061205.1 MEALZ_RS15785 (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.20447.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-120 387.2 0.0 4.3e-120 387.0 0.0 1.0 1 lcl|NCBI__GCF_000968535.2:WP_046061205.1 MEALZ_RS15785 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_046061205.1 MEALZ_RS15785 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.0 0.0 4.3e-120 4.3e-120 1 334 [. 13 345 .. 13 354 .. 0.96 Alignments for each domain: == domain 1 score: 387.0 bits; conditional E-value: 4.3e-120 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 y++++g+ ll+k+ +++ ++++++++t+e+v+ l+ +++++ l++ + v+++v+pdge++K+l+ + lcl|NCBI__GCF_000968535.2:WP_046061205.1 13 YPIYIGSRLLEKADLLTRHiRSKQILIVTNETVAPLYLQQVLDNLSD--FVVETVVLPDGEQYKTLDYL 79 67899999999776655556669**********************87..99****************** PP TIGR01357 69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137 +++ d+ll++k++r+ l+a+GGGv+gD++GF+Aa y+RGi+++q+PTtlla+vDssvGGKtg+n++lg lcl|NCBI__GCF_000968535.2:WP_046061205.1 80 NRIFDTLLAHKFSRNASLIALGGGVIGDMGGFAAACYQRGIPFIQIPTTLLAQVDSSVGGKTGVNHSLG 148 ********************************************************************* PP TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206 kN+iGafyqP+ V+ d++vl+tl++r+l++G+aEviK+gli d ++f++le+n ++ll++ + eal+++ lcl|NCBI__GCF_000968535.2:WP_046061205.1 149 KNMIGAFYQPQCVIADMSVLSTLDDRQLSAGIAEVIKYGLIRDPDFFSWLENNLESLLDR-DAEALAHA 216 *******************************************************99986.66****** PP TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274 ++rs++ KaevV++Deke+ +Ra+LN+GHt+gHaiE+ ++y+ + HGeaVaiG ++a ls+++g l lcl|NCBI__GCF_000968535.2:WP_046061205.1 217 VERSCRNKAEVVAADEKEADVRATLNLGHTFGHAIETGMGYGsYLHGEAVAIGTCQAADLSRRKGWLTD 285 ********************************************************************* PP TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasev 334 ++er+++l+k++ lp++ + l+++ +++ + DKKn +++i+l+ll++iG+a+l v lcl|NCBI__GCF_000968535.2:WP_046061205.1 286 ADVERIIRLFKRARLPVEPPVALDANRFIELMAVDKKNVDGNIRLILLKSIGEATLPVGV 345 *****************************************************9987544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (361 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: 7.16 // [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