Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 17452 b3389 3-dehydroquinate synthase (NCBI)
Query= BRENDA::P07639 (362 letters) >FitnessBrowser__Keio:17452 Length = 362 Score = 708 bits (1827), Expect = 0.0 Identities = 362/362 (100%), Positives = 362/362 (100%) Query: 1 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA Sbjct: 1 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60 Query: 61 GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120 GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR Sbjct: 61 GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120 Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS Sbjct: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180 Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR Sbjct: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240 Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA Sbjct: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300 Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ Sbjct: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADCQ 360 Query: 361 SA 362 SA Sbjct: 361 SA 362 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: 569 Number of extensions: 6 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: 362 Length adjustment: 29 Effective length of query: 333 Effective length of database: 333 Effective search space: 110889 Effective search space used: 110889 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 17452 b3389 (3-dehydroquinate synthase (NCBI))
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.17559.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-127 409.3 0.0 7.7e-127 409.2 0.0 1.0 1 lcl|FitnessBrowser__Keio:17452 b3389 3-dehydroquinate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17452 b3389 3-dehydroquinate synthase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.2 0.0 7.7e-127 7.7e-127 1 341 [. 13 354 .. 13 357 .. 0.97 Alignments for each domain: == domain 1 score: 409.2 bits; conditional E-value: 7.7e-127 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldqllee 78 y++++ +gl+++ ++ l + ++++++t+e+++ l+ +k++ +l+++gv+v+ +++pdge++Ksl+++ ++ ++ll++ lcl|FitnessBrowser__Keio:17452 13 YPITIASGLFNEPASFLPLkSGEQVMLVTNETLAPLYLDKVRGVLEQAGVNVDSVILPDGEQYKSLAVLDTVFTALLQK 91 67999999999888888763459******************************************************** PP TIGR01357 79 klerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVlidlkvl 157 + r+++lva+GGGvvgDl+GF+Aa+y+RG+r++qvPTtll++vDssvGGKt++n+plgkN+iGafyqP V++dl++l lcl|FitnessBrowser__Keio:17452 92 PHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCL 170 ******************************************************************************* PP TIGR01357 158 etlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRalLNfGHt 236 +tlp rel++G+aEviK+g+i d ++f++le+n ++ll+l + a++ +i+r++e+KaevV++De+e+glRalLN+GHt lcl|FitnessBrowser__Keio:17452 171 KTLPPRELASGLAEVIKYGIILDGAFFNWLEENLDALLRL-DGPAMAYCIRRCCELKAEVVAADERETGLRALLNLGHT 248 ***********************************99986.66************************************ PP TIGR01357 237 lgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellkallkDKKneg 314 +gHaiEa+++y+ + HGeaVa Gmv++a++se+lg++++ +++r+++llk++glp++ ++++s++++l ++l+DKK + lcl|FitnessBrowser__Keio:17452 249 FGHAIEAEMGYGnWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAGLPVNGPREMSAQAYLPHMLRDKKVLA 327 ******************************************************************************* PP TIGR01357 315 skiklvlleeiGkaalasevteeelle 341 ++++l+l+ +iGk +++s v++e +l+ lcl|FitnessBrowser__Keio:17452 328 GEMRLILPLAIGKSEVRSGVSHELVLN 354 ****************99988887766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (362 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.12 // [ok]
This GapMind analysis is from Apr 09 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