Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate NP_347530.1 CA_C0894 3-dehydroquinate synthase
Query= curated2:Q97KM3 (356 letters) >NCBI__GCF_000008765.1:NP_347530.1 Length = 356 Score = 708 bits (1827), Expect = 0.0 Identities = 356/356 (100%), Positives = 356/356 (100%) Query: 1 MKTLEMELGQNSYSIFIEKGIMNDIGKRISKLYSGEKIVLITDDNVNKFYGEKLEKNIKD 60 MKTLEMELGQNSYSIFIEKGIMNDIGKRISKLYSGEKIVLITDDNVNKFYGEKLEKNIKD Sbjct: 1 MKTLEMELGQNSYSIFIEKGIMNDIGKRISKLYSGEKIVLITDDNVNKFYGEKLEKNIKD 60 Query: 61 FGYDVFKIVIKAGEKSKNIKTLTDIYSRLAEFRITRSDLIVTLGGGVVGDIGGFAAATYL 120 FGYDVFKIVIKAGEKSKNIKTLTDIYSRLAEFRITRSDLIVTLGGGVVGDIGGFAAATYL Sbjct: 61 FGYDVFKIVIKAGEKSKNIKTLTDIYSRLAEFRITRSDLIVTLGGGVVGDIGGFAAATYL 120 Query: 121 RGISYIQIPTSLLAQIDSSIGGKVAVDLEQGKNLVGNFYQPKAVFIDPLFLKTLDIRFLH 180 RGISYIQIPTSLLAQIDSSIGGKVAVDLEQGKNLVGNFYQPKAVFIDPLFLKTLDIRFLH Sbjct: 121 RGISYIQIPTSLLAQIDSSIGGKVAVDLEQGKNLVGNFYQPKAVFIDPLFLKTLDIRFLH 180 Query: 181 DGMGEVIKYGAIRDGELFKRLEEFKDDNELMDNIEYVIHACCRIKKQVVENDEKDNGERM 240 DGMGEVIKYGAIRDGELFKRLEEFKDDNELMDNIEYVIHACCRIKKQVVENDEKDNGERM Sbjct: 181 DGMGEVIKYGAIRDGELFKRLEEFKDDNELMDNIEYVIHACCRIKKQVVENDEKDNGERM 240 Query: 241 ILNFGHTIGHAVEEFFHYEKFTHGECVAYGMYSITKNSERLGITKEGTTEKLKNIIKKYS 300 ILNFGHTIGHAVEEFFHYEKFTHGECVAYGMYSITKNSERLGITKEGTTEKLKNIIKKYS Sbjct: 241 ILNFGHTIGHAVEEFFHYEKFTHGECVAYGMYSITKNSERLGITKEGTTEKLKNIIKKYS 300 Query: 301 LPFNIDNLKNERIYEIAALDKKSRGKFINLVLLKDIGDCFIEKVESKETYKYLRVV 356 LPFNIDNLKNERIYEIAALDKKSRGKFINLVLLKDIGDCFIEKVESKETYKYLRVV Sbjct: 301 LPFNIDNLKNERIYEIAALDKKSRGKFINLVLLKDIGDCFIEKVESKETYKYLRVV 356 Lambda K H 0.320 0.141 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: 692 Number of extensions: 17 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: 356 Length of database: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate NP_347530.1 CA_C0894 (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.5262.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-119 385.6 0.9 1.3e-119 385.4 0.9 1.0 1 lcl|NCBI__GCF_000008765.1:NP_347530.1 CA_C0894 3-dehydroquinate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008765.1:NP_347530.1 CA_C0894 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 385.4 0.9 1.3e-119 1.3e-119 1 339 [. 13 349 .. 13 354 .. 0.97 Alignments for each domain: == domain 1 score: 385.4 bits; conditional E-value: 1.3e-119 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvak 70 y++ +++g+++ + + +++ + +k+v+itd++v+k ++ekle+ k+ g+ v+++v+++ge+sK+++t+++ lcl|NCBI__GCF_000008765.1:NP_347530.1 13 YSIFIEKGIMNDIGKRISKlySGEKIVLITDDNVNKFYGEKLEKNIKDFGYDVFKIVIKAGEKSKNIKTLTD 84 6899***************7656************************************************* PP TIGR01357 71 lldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliG 142 ++++l+e ++r++++v++GGGvvgD++GF+AatylRGi+++q+PT+lla++Dss+GGK++++l++gkNl+G lcl|NCBI__GCF_000008765.1:NP_347530.1 85 IYSRLAEFRITRSDLIVTLGGGVVGDIGGFAAATYLRGISYIQIPTSLLAQIDSSIGGKVAVDLEQGKNLVG 156 ************************************************************************ PP TIGR01357 143 afyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievK 214 fyqPkaV+id+ +l+tl+ r l +Gm+EviK+g+i d elf++le+++++ + ++ +e +i ++++K lcl|NCBI__GCF_000008765.1:NP_347530.1 157 NFYQPKAVFIDPLFLKTLDIRFLHDGMGEVIKYGAIRDGELFKRLEEFKDDNE---LMDNIEYVIHACCRIK 225 ************************************************99544...3599************ PP TIGR01357 215 aevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallk 285 ++vVe+Dek++g R++LNfGHt+gHa+E +++y+ ++HGe+Va+Gm +k se+lg++k+ +e+l++++k lcl|NCBI__GCF_000008765.1:NP_347530.1 226 KQVVENDEKDNGERMILNFGHTIGHAVEEFFHYEkFTHGECVAYGMYSITKNSERLGITKEGTTEKLKNIIK 297 ************************************************************************ PP TIGR01357 286 klglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeel 339 k++lp+++ + l+ e +++ DKK++g+ i+lvll++iG+++++ +v ++e+ lcl|NCBI__GCF_000008765.1:NP_347530.1 298 KYSLPFNIDN-LKNERIYEIAALDKKSRGKFINLVLLKDIGDCFIE-KVESKET 349 *********7.**********************************9.7766665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (356 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: 10.46 // [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