Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type I DHQase; Type I dehydroquinase; DHQ1; EC 4.2.1.10 (characterized)
to candidate WP_010876205.1 MTH_RS02630 3-dehydroquinase
Query= SwissProt::Q6LXF7 (218 letters) >NCBI__GCF_000008645.1:WP_010876205.1 Length = 221 Score = 134 bits (338), Expect = 1e-36 Identities = 88/218 (40%), Positives = 129/218 (59%), Gaps = 13/218 (5%) Query: 2 ICIPVIDKDVSDAINSAKEALKYG-DIVEFRIDLLN---DVNFKDIEEFSKIPSIITIRA 57 IC+PV +K + SA A+ G DI+E RID L +VN +++ E P I T R+ Sbjct: 5 ICVPVFEKTAPEVTESAGRAIDAGADILEIRIDGLQNPGEVNIRELIEDIGFPVIATNRS 64 Query: 58 EWEGGAWRKSNEERIELLKNAIKNNAKFIDIELKEEK-NLELVKYRNEIGSTTKIIVSYH 116 EGG + S +ERI+LL A + A F+DIEL + ++E V GS + IVSYH Sbjct: 65 PVEGGHFSGSEDERIKLLMAAAEV-ADFVDIELSSAREDIERVT-----GSARRSIVSYH 118 Query: 117 DFEKTPEIDELIDVVEKELKIGDIAKFATFAHSKEDTLKILNLMNRYSGKIIAIGMGESG 176 +F +TP ++ L+ +V ++GDIAK A + DTL +L L+ + +AI MGE G Sbjct: 119 NFRETPSLEALLRIVRMAKEMGDIAKVAVMPENLADTLVVLQLLT-FEEDTVAISMGELG 177 Query: 177 KLTRILGLDFGSILTFASMGGKASAPGQVDVKKLKEIL 214 K TR+ FGS +TFASM G+ +APGQ+DV ++++ Sbjct: 178 KYTRVAAALFGSPITFASM-GRGTAPGQMDVDVTRKMI 214 Lambda K H 0.316 0.137 0.377 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: 137 Number of extensions: 11 Number of successful extensions: 5 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: 218 Length of database: 221 Length adjustment: 22 Effective length of query: 196 Effective length of database: 199 Effective search space: 39004 Effective search space used: 39004 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 45 (21.9 bits)
Align candidate WP_010876205.1 MTH_RS02630 (3-dehydroquinase)
to HMM TIGR01093 (aroD: 3-dehydroquinate dehydratase, type I (EC 4.2.1.10))
# 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/TIGR01093.hmm # target sequence database: /tmp/gapView.27357.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01093 [M=229] Accession: TIGR01093 Description: aroD: 3-dehydroquinate dehydratase, type I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-55 173.7 0.0 3.5e-55 173.6 0.0 1.0 1 lcl|NCBI__GCF_000008645.1:WP_010876205.1 MTH_RS02630 3-dehydroquinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008645.1:WP_010876205.1 MTH_RS02630 3-dehydroquinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 173.6 0.0 3.5e-55 3.5e-55 1 228 [. 4 213 .. 4 214 .. 0.94 Alignments for each domain: == domain 1 score: 173.6 bits; conditional E-value: 3.5e-55 TIGR01093 1 kilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqk 69 ki+vp+ +k++ e++e + + + gaDi+E+R+D l+++++ + + +++e + p+i T R+ lcl|NCBI__GCF_000008645.1:WP_010876205.1 4 KICVPVFEKTAPEVTESAGRAIDAGADILEIRIDGLQNPGEVN-IRELIEDI-----GFPVIATNRSPV 66 79****************************************7.99999999.....8*********** PP TIGR01093 70 eGGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeel 138 eGG+f g+e+er+++l++a+e d+vDiEl+++ e ++ ++ + + i+S+H+f++tps e l lcl|NCBI__GCF_000008645.1:WP_010876205.1 67 EGGHFSGSEDERIKLLMAAAEVA--DFVDIELSSAREDIERVTG----SARRSIVSYHNFRETPSLEAL 129 ****************8888766..*********9998876555....77888**************** PP TIGR01093 139 verlekaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvlt 207 ++++ a+++ +Di+K+avm++++ D l +l++++ + +a+sMge Gk +Rv++a++gs +t lcl|NCBI__GCF_000008645.1:WP_010876205.1 130 LRIVRMAKEM-GDIAKVAVMPENLADTLVVLQLLTFE-----EDTVAISMGELGKYTRVAAALFGSPIT 192 **********.*********************99555.....69************************* PP TIGR01093 208 fgslgkasAPGQisvkelrel 228 f+s+g APGQ++v+ r++ lcl|NCBI__GCF_000008645.1:WP_010876205.1 193 FASMGRGTAPGQMDVDVTRKM 213 ****************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (221 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: 6.46 // [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