Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_028313194.1 G491_RS0100540 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000429905.1:WP_028313194.1 Length = 340 Score = 209 bits (533), Expect = 7e-59 Identities = 134/328 (40%), Positives = 190/328 (57%), Gaps = 18/328 (5%) Query: 29 LPLKSGEQVMLVTNETLAPLY--LDKVRGVLEQAGVNVDSVILPDGEQYKSLAVLDTVFT 86 L L G+ V ++T+ET+ LY L VLE + +GE K+L + + Sbjct: 27 LHLPKGKTV-IITDETVNDLYGNLFPACPVLE----------IGEGEGNKTLDTVARLMG 75 Query: 87 ALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQVPTTLLSQVDSSVGGKTAVN 146 L+ R +V +GGG+V D+TGF A++Y RGV F PTTLL+QVD+SVGGK VN Sbjct: 76 ELVGLGLDRSCFIVGIGGGIVCDVTGFVASTYLRGVDFGFCPTTLLAQVDASVGGKNGVN 135 Query: 147 HPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGLAEVIKYGIILDGAFFNWLEENLDA 206 + KNM+G F QP+ V+ D LK+LP EL +G AE++K+G I D + F +LE+N Sbjct: 136 YKGYKNMVGVFNQPSFVLCDPKVLKSLPQDELTNGFAEIVKHGAIRDESHFTFLEDNKAK 195 Query: 207 LLRLDGPAMAYCIRRCCELKAEVVAADERETGLRALLNLGHTFGHAIEAEMGYGNWLHGE 266 L LD MA+ I +KA+VV DE+ETG+R +LN GHTFGHA+E G HG+ Sbjct: 196 ALSLDSEFMAHLIYDSIAIKADVVNQDEKETGIRKILNFGHTFGHALEKTAGVS---HGK 252 Query: 267 AVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGLPVNGPREMSAQAYLPHMLRDKKVL 326 AV+AGMVMA S G ++++RI LLK GLP+ E+ L + +DKK L Sbjct: 253 AVSAGMVMACNLSMDRGLLKESDSERIKKLLKDLGLPLR--IEVDPAKALDALAKDKKKL 310 Query: 327 AGEMRLILPLAIGKSEVRSGVSHELVLN 354 ++ +L A+G++ V + +L N Sbjct: 311 GDAIQFVLLKALGEAVVETISIRDLETN 338 Lambda K H 0.320 0.136 0.392 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: 248 Number of extensions: 10 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: 340 Length adjustment: 29 Effective length of query: 333 Effective length of database: 311 Effective search space: 103563 Effective search space used: 103563 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_028313194.1 G491_RS0100540 (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.27686.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-109 350.0 0.1 9e-109 349.7 0.1 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028313194.1 G491_RS0100540 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028313194.1 G491_RS0100540 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.7 0.1 9e-109 9e-109 16 332 .. 28 329 .. 14 339 .. 0.93 Alignments for each domain: == domain 1 score: 349.7 bits; conditional E-value: 9e-109 TIGR01357 16 elaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqlleeklerks 84 +l + k+v+itde+v++l+++ + + vl + +ge +K+l+tva+l+ +l+ +l+r+ lcl|NCBI__GCF_000429905.1:WP_028313194.1 28 HLP--KGKTVIITDETVNDLYGNLFPACP--------VLEIGEGEGNKTLDTVARLMGELVGLGLDRSC 86 333..37899***********99998877........689***************************** PP TIGR01357 85 vlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlid 153 +v+iGGG+v D++GFvA+tylRG+++ PTtlla+vD+svGGK+g+n ++ kN++G f qP++Vl+d lcl|NCBI__GCF_000429905.1:WP_028313194.1 87 FIVGIGGGIVCDVTGFVASTYLRGVDFGFCPTTLLAQVDASVGGKNGVNYKGYKNMVGVFNQPSFVLCD 155 ********************************************************************* PP TIGR01357 154 lkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDe 222 +kvl++lp++el +G+aE++Khg+i d++ f++le+n+++ l+l + e +++li +si +Ka+vV++De lcl|NCBI__GCF_000429905.1:WP_028313194.1 156 PKVLKSLPQDELTNGFAEIVKHGAIRDESHFTFLEDNKAKALSL-DSEFMAHLIYDSIAIKADVVNQDE 223 **************************************999976.55********************** PP TIGR01357 223 kesglRalLNfGHtlgHaiEallkyklsHGeaVaiGmvveaklseklgllkaellerlvallkklglpt 291 ke+g+R++LNfGHt+gHa+E++++ +sHG+aV+ Gmv++ +ls gllk++++er+++llk lglp lcl|NCBI__GCF_000429905.1:WP_028313194.1 224 KETGIRKILNFGHTFGHALEKTAG--VSHGKAVSAGMVMACNLSMDRGLLKESDSERIKKLLKDLGLPL 290 *********************665..******************************************* PP TIGR01357 292 klkkklsveellkallkDKKnegskiklvlleeiGkaalas 332 +++ ++ ++l+al kDKK+ g+ i++vll+++G+a++++ lcl|NCBI__GCF_000429905.1:WP_028313194.1 291 RIE--VDPAKALDALAKDKKKLGDAIQFVLLKALGEAVVET 329 **9..7******************************99884 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (340 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.86 // [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