Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011883026.1 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000016205.1:WP_011883026.1 Length = 359 Score = 370 bits (949), Expect = e-107 Identities = 191/334 (57%), Positives = 232/334 (69%), Gaps = 1/334 (0%) Query: 1 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60 M + V LG+R+YPI I +GL F P +G V +VTN T+ PLY D +R L Sbjct: 1 MITVNVDLGDRAYPIHIGAGLIGRTELFAPHINGSSVTIVTNTTVDPLYGDALRAALAPL 60 Query: 61 GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120 G V +V+LPDGE YK+ L+ +F LL + R TTL+ALGGGV+GD+TGFAAA Y R Sbjct: 61 GKRVSTVVLPDGEAYKNWETLNLIFDGLLTERADRKTTLIALGGGVIGDMTGFAAACYMR 120 Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180 GV FIQVPTTLLSQVDSSVGGKT +NHPLGKNMIGAFYQP +VV D+ L TLP RELA+ Sbjct: 121 GVPFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPQAVVADIGALATLPDRELAA 180 Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240 G+AEVIK G I D FF+W+E N+DAL R + + + ++R CE+KA VVAADERE GLR Sbjct: 181 GIAEVIKTGAIADAEFFDWIEANVDALNRREPAVLVHAVKRSCEIKASVVAADEREGGLR 240 Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300 A+LN GHTFGHAIEA +GYG WLHGEAV GMVMA S RLG A QR+ ++ A Sbjct: 241 AILNFGHTFGHAIEAGLGYGEWLHGEAVGCGMVMAGDLSVRLGLLDEASRQRLDAVIAAA 300 Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLIL 334 LPV+GP + Y+ M DKK AG ++ IL Sbjct: 301 RLPVSGP-ALGEARYMDLMRVDKKAEAGAIKFIL 333 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: 346 Number of extensions: 5 Number of successful extensions: 1 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: 359 Length adjustment: 29 Effective length of query: 333 Effective length of database: 330 Effective search space: 109890 Effective search space used: 109890 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_011883026.1 (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.16859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-120 388.2 0.0 2.2e-120 387.9 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011883026.1 3-dehydroquinate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011883026.1 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.9 0.0 2.2e-120 2.2e-120 1 331 [. 13 343 .. 13 354 .. 0.95 Alignments for each domain: == domain 1 score: 387.9 bits; conditional E-value: 2.2e-120 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g gl+ ++ e +a + s++ ++t+ +v+ l+++ l++al+ lg +v ++v+pdge +K++et lcl|NCBI__GCF_000016205.1:WP_011883026.1 13 YPIHIGAGLIGRT-ELFAPhiNGSSVTIVTNTTVDPLYGDALRAALAPLGKRVSTVVLPDGEAYKNWET 80 6799999999854.3333334569********************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++ + d ll+e ++rk++l+a+GGGv+gD++GF+Aa y+RG++++qvPTtll++vDssvGGKtgin+pl lcl|NCBI__GCF_000016205.1:WP_011883026.1 81 LNLIFDGLLTERADRKTTLIALGGGVIGDMTGFAAACYMRGVPFIQVPTTLLSQVDSSVGGKTGINHPL 149 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGafyqP+aV+ d+ l+tlp+rel++G+aEviK+g+iadae+f+++e n ++l+++ e ++l + lcl|NCBI__GCF_000016205.1:WP_011883026.1 150 GKNMIGAFYQPQAVVADIGALATLPDRELAAGIAEVIKTGAIADAEFFDWIEANVDALNRR-EPAVLVH 217 ********************************************************88875.66***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 ++krs+e+Ka+vV++De+e glRa+LNfGHt+gHaiEa l+y+ + HGeaV +Gmv++ ls +lgll+ lcl|NCBI__GCF_000016205.1:WP_011883026.1 218 AVKRSCEIKASVVAADEREGGLRAILNFGHTFGHAIEAGLGYGeWLHGEAVGCGMVMAGDLSVRLGLLD 286 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaala 331 + ++rl a++ ++ lp++ + l +++ + DKK+e++ ik++ll+++G++ +a lcl|NCBI__GCF_000016205.1:WP_011883026.1 287 EASRQRLDAVIAAARLPVSGPA-LGEARYMDLMRVDKKAEAGAIKFILLKRFGDTLIA 343 *********************7.99999*************************99877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (359 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: 9.02 // [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