Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_035236293.1 Q366_RS02585 3-dehydroquinate synthase
Query= curated2:B5E8I9 (362 letters) >NCBI__GCF_000745975.1:WP_035236293.1 Length = 345 Score = 233 bits (594), Expect = 6e-66 Identities = 129/280 (46%), Positives = 177/280 (63%), Gaps = 4/280 (1%) Query: 70 VTLPDGEGYKNSATLNLIYDGLVDASLDRGSFILALGGGVIGDMAGFAAASYLRGIPFVQ 129 +T+ GE K +T+ I +V A DR SF+LA+GGG++ D+AGFAA+ +LRGI F Sbjct: 57 ITIGTGEKIKVLSTVEYILREMVKAGCDRSSFLLAIGGGIVCDIAGFAASVFLRGIRFGF 116 Query: 130 IPTTLLSQVDSSVGGKTGINHPRGKNLIGAFYQPKAVLIDVATLDTLPKREFLSGLGEIV 189 + T+LLSQVD+SVGGK G+N KN++G F QP+ VL D+ L TLP+ E +GL EIV Sbjct: 117 VSTSLLSQVDASVGGKNGVNLDAFKNMVGVFSQPQFVLCDIDMLSTLPEMEISNGLAEIV 176 Query: 190 KYGAVLDGGFFDFLEKNAKLLLARDKEALIQAVSRSCAIKAKVVAEDEREGGVRAVLNYG 249 K+G + D +F+E N LA D+E + + V+ S AIK++VV DERE G R LN+G Sbjct: 177 KHGLIKDISLLEFIENNRDKALALDRETVFRMVADSVAIKSRVVQADEREAGERRKLNFG 236 Query: 250 HTLGHAVETLTGYTRYLHGEAVAIGMVQAARLSQHYGFCSQADRERIEALVVALGLPTEL 309 HT+GHA E L HG AVA GMV AA SQ G+ +Q D +RI+ L+ LGLP Sbjct: 237 HTIGHAFEKLNPCG---HGRAVAAGMVAAAAFSQQKGYINQGDVDRIKDLLSGLGLPVAF 293 Query: 310 PSFPPQQYREALSHDKKVRDKGLLFICNQGIGAYRMERLT 349 FP +Q EA S DKK + L F+ IG ++++++ Sbjct: 294 -DFPAEQIIEAASRDKKKQGHNLFFVFLGQIGQAKVDKIS 332 Lambda K H 0.320 0.139 0.398 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: 340 Number of extensions: 12 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: 362 Length of database: 345 Length adjustment: 29 Effective length of query: 333 Effective length of database: 316 Effective search space: 105228 Effective search space used: 105228 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_035236293.1 Q366_RS02585 (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.6514.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-101 323.7 0.1 9.5e-101 323.4 0.1 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035236293.1 Q366_RS02585 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035236293.1 Q366_RS02585 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 323.4 0.1 9.5e-101 9.5e-101 3 335 .. 16 332 .. 14 340 .. 0.93 Alignments for each domain: == domain 1 score: 323.4 bits; conditional E-value: 9.5e-101 TIGR01357 3 vkvgegllkklveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 ++vge+l +++ ++l + + +v++tde++ k++++ + + + v+++ ge++K l+tv+ + lcl|NCBI__GCF_000745975.1:WP_035236293.1 16 IHVGESL-SRVGDYLPD-QGPVVIVTDENILKHYGASFPAGH--------VITIGTGEKIKVLSTVEYI 74 5666443.446667665.678999999999999988877655........79***************** PP TIGR01357 72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNl 140 l+++++++++r+s l+aiGGG+v D+aGF+A+++lRGir+ v+T+ll++vD+svGGK+g+nl+ kN+ lcl|NCBI__GCF_000745975.1:WP_035236293.1 75 LREMVKAGCDRSSFLLAIGGGIVCDIAGFAASVFLRGIRFGFVSTSLLSQVDASVGGKNGVNLDAFKNM 143 ********************************************************************* PP TIGR01357 141 iGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikr 209 +G f qP++Vl+d+++l+tlpe e+++G+aE++Khgli+d +l+e++e+n ++ l l + e++ +++++ lcl|NCBI__GCF_000745975.1:WP_035236293.1 144 VGVFSQPQFVLCDIDMLSTLPEMEISNGLAEIVKHGLIKDISLLEFIENNRDKALAL-DRETVFRMVAD 211 ****************************************************99986.559******** PP TIGR01357 210 sievKaevVeeDekesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaelle 278 s+ +K++vV++De+e+g R+ LNfGHt+gHa E+l + HG+aVa Gmv +a +s+++g++++ +++ lcl|NCBI__GCF_000745975.1:WP_035236293.1 212 SVAIKSRVVQADEREAGERRKLNFGHTIGHAFEKLNP--CGHGRAVAAGMVAAAAFSQQKGYINQGDVD 278 **********************************655..99**************************** PP TIGR01357 279 rlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevt 335 r+++ll+ lglp+ + + +e++++a ++DKK++g+++ +v+l +iG+a+++ +++ lcl|NCBI__GCF_000745975.1:WP_035236293.1 279 RIKDLLSGLGLPVAFD--FPAEQIIEAASRDKKKQGHNLFFVFLGQIGQAKVD-KIS 332 *************998..7*******************************998.443 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (345 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: 00:00:00.00 # Mc/sec: 12.35 // [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