Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_006747099.1 THITH_RS14475 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000227685.2:WP_006747099.1 Length = 365 Score = 416 bits (1070), Expect = e-121 Identities = 204/356 (57%), Positives = 274/356 (76%), Gaps = 5/356 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 +EV+LG RSYPI+IG+GLL +PDLL H+ G+R++VVTN TVAPL+ D+ + AL +G Sbjct: 4 LEVELGPRSYPIHIGSGLLARPDLLAPHLRGQRLVVVTNETVAPLHGDR-LRALLEGQDV 62 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 +E LPDGE K + T+ + + +E+RLDR T +A GGGV+GD+ G+AAA Y RG Sbjct: 63 TWIE---LPDGEAHKTLATVEAILTRMLEARLDRGSTLIAFGGGVVGDIAGFAAAIYQRG 119 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 ++FIQ+PTT+++QVDSSVGGKTG+NHPLGKNMIGAF+QP+ V+IDT++L TLP REL +G Sbjct: 120 IDFIQVPTTLLSQVDSSVGGKTGVNHPLGKNMIGAFHQPRAVIIDTESLATLPLRELRAG 179 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 +AE+IKYGLI+DA+FF W EQ++ LLA DP T AI RSC KA+VV+ DE+ESG RA Sbjct: 180 VAEIIKYGLIQDADFFAWLEQHIEALLALDPQVTTEAIYRSCACKAEVVAADERESGRRA 239 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 LNLGHTFGHA+E G+GYG+WLHGEAV G MA MS ++GW+ + +R +K++++A Sbjct: 240 LLNLGHTFGHAIEAGMGYGEWLHGEAVGTGMAMAARMSEQMGWLQPAERERAEKLIERAG 299 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436 L SPP +T E F+ +MA+DKKV DG+LRL+LL+ ++G+ V TGD+ ALD TL Sbjct: 300 LALSPPPELTAERFRELMAIDKKVMDGQLRLVLLR-AIGSAVVTGDFPPDALDATL 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: 399 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_006747099.1 THITH_RS14475 (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.7682.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-122 393.0 0.0 7.4e-122 392.8 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006747099.1 THITH_RS14475 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006747099.1 THITH_RS14475 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 392.8 0.0 7.4e-122 7.4e-122 1 338 [. 13 349 .. 13 354 .. 0.95 Alignments for each domain: == domain 1 score: 392.8 bits; conditional E-value: 7.4e-122 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g+gll++ la + ++lvv+t+e+v+ l++++l+++l+ g+ v+++ +pdge +K+l+t lcl|NCBI__GCF_000227685.2:WP_006747099.1 13 YPIHIGSGLLARPD-LLAPhlRGQRLVVVTNETVAPLHGDRLRALLE--GQDVTWIELPDGEAHKTLAT 78 67999999998553.334334569**********************6..7******************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 v+++l+++le+ l+r s+l+a+GGGvvgD+aGF+Aa+y+RGi+++qvPTtll++vDssvGGKtg+n+pl lcl|NCBI__GCF_000227685.2:WP_006747099.1 79 VEAILTRMLEARLDRGSTLIAFGGGVVGDIAGFAAAIYQRGIDFIQVPTTLLSQVDSSVGGKTGVNHPL 147 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGaf+qP+aV+id++ l+tlp relr+G+aE+iK+gli+da++f++le++ ++ll l + ++++e lcl|NCBI__GCF_000227685.2:WP_006747099.1 148 GKNMIGAFHQPRAVIIDTESLATLPLRELRAGVAEIIKYGLIQDADFFAWLEQHIEALLAL-DPQVTTE 215 ********************************************************99986.55***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i rs+ +KaevV++De+esg RalLN+GHt+gHaiEa ++y+ + HGeaV +Gm+++a++se++g l+ lcl|NCBI__GCF_000227685.2:WP_006747099.1 216 AIYRSCACKAEVVAADERESGRRALLNLGHTFGHAIEAGMGYGeWLHGEAVGTGMAMAARMSEQMGWLQ 284 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteee 338 + ++er ++l++++gl + +++l++e + + + DKK +++++lvll++iG+a+++ +++ ++ lcl|NCBI__GCF_000227685.2:WP_006747099.1 285 PAERERAEKLIERAGLALSPPPELTAERFRELMAIDKKVMDGQLRLVLLRAIGSAVVTGDFPPDA 349 *******************************************************9988876655 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.60 // [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