Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_035245909.1 G494_RS0108075 type I 3-dehydroquinate dehydratase
Query= curated2:Q6AIT8 (226 letters) >NCBI__GCF_000429965.1:WP_035245909.1 Length = 233 Score = 173 bits (439), Expect = 2e-48 Identities = 96/218 (44%), Positives = 133/218 (61%), Gaps = 3/218 (1%) Query: 6 ICVSL--GQPTMPQALEASLRIFGADVIEVRLDYIDVPEIDPFVESLATDLLFTCRPTWE 63 +CVSL G+P Q E ADV+E+RLD ++ P+I ++ ++ LLFT RP WE Sbjct: 8 VCVSLAGGEPG-GQLQELQRLAPRADVVEIRLDTLENPDIGSWLATMERPLLFTNRPAWE 66 Query: 64 GGLFAGTEEDRLALLAEAVRAGAAYIDLELRSAEESHQYLRTYLAERETELILSYHDFES 123 GG F+G EE RLALLA A+ AAYIDLEL + E L ++ T++I+S HDF++ Sbjct: 67 GGNFSGPEEQRLALLARAIELDAAYIDLELATEPERRLALIDMARDKTTQVIVSSHDFKA 126 Query: 124 TATLAKLTGIIDQMQDAGADIGKLITTANSAADVVRVFQVLEYAAKKGLPLIAFCMGEAG 183 T A L ++QM +GAD GK++TTA + DV+RV +LE A + PL AFCMG G Sbjct: 127 TPPQADLRQTLEQMMASGADCGKIVTTAQDSDDVIRVLGLLEIAHQAAFPLSAFCMGGPG 186 Query: 184 AVSRVASCDLGGYMTYCCADGAEVTAAGQITISEMRGI 221 +SR A LGG+M Y D A TA GQ++ + + + Sbjct: 187 RISRFAGLYLGGFMNYVALDQASATAPGQLSAAHCQSL 224 Lambda K H 0.321 0.136 0.393 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: 136 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: 226 Length of database: 233 Length adjustment: 23 Effective length of query: 203 Effective length of database: 210 Effective search space: 42630 Effective search space used: 42630 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 (21.9 bits) S2: 46 (22.3 bits)
Align candidate WP_035245909.1 G494_RS0108075 (type I 3-dehydroquinate dehydratase)
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.5097.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-49 154.8 0.0 2.4e-49 154.5 0.0 1.1 1 lcl|NCBI__GCF_000429965.1:WP_035245909.1 G494_RS0108075 type I 3-dehydroq Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429965.1:WP_035245909.1 G494_RS0108075 type I 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 154.5 0.0 2.4e-49 2.4e-49 2 226 .. 8 222 .. 7 225 .. 0.91 Alignments for each domain: == domain 1 score: 154.5 bits; conditional E-value: 2.4e-49 TIGR01093 2 ilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqke 70 ++v+l+ + +l+el+ + aD+vE+R+D l+++ + + + pl++T R ++e lcl|NCBI__GCF_000429965.1:WP_035245909.1 8 VCVSLAGGEPGGQLQELQRLA-PRADVVEIRLDTLENPDIGS----WL-----ATMERPLLFTNRPAWE 66 577777777888899999988.77*************99886....22.....33589*********** PP TIGR01093 71 GGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelv 139 GG+f g ee+rl++l +aie + ++D+El++e e +li a ++ t++i+S+Hdf+ tp++++l+ lcl|NCBI__GCF_000429965.1:WP_035245909.1 67 GGNFSGPEEQRLALLARAIELD-AAYIDLELATEPERRLALIDMARDKTTQVIVSSHDFKATPPQADLR 134 *********************9.99******************************************** PP TIGR01093 140 erlekaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltf 208 + le++ + +aD Ki+++a++ +Dv+++l ++ +++++ + pl a+ Mg G isR +g +lg+ + + lcl|NCBI__GCF_000429965.1:WP_035245909.1 135 QTLEQMMASGADCGKIVTTAQDSDDVIRVLGLL-EIAHQAAFPLSAFCMGGPGRISRFAGLYLGGFMNY 202 *****************************9998.5655779**************************** PP TIGR01093 209 gslgkas..APGQisvkelr 226 +l++as APGQ+s ++ + lcl|NCBI__GCF_000429965.1:WP_035245909.1 203 VALDQASatAPGQLSAAHCQ 222 *777655228****998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (233 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: 00:00:00.00 # Mc/sec: 9.94 // [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