Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type I DHQase; Type I dehydroquinase; DHQ1; EC 4.2.1.10 (characterized)
to candidate WP_013644232.1 METBO_RS03210 type I 3-dehydroquinate dehydratase
Query= SwissProt::Q6LXF7 (218 letters) >NCBI__GCF_000191585.1:WP_013644232.1 Length = 225 Score = 140 bits (353), Expect = 2e-38 Identities = 86/218 (39%), Positives = 134/218 (61%), Gaps = 13/218 (5%) Query: 2 ICIPVIDKDVSDAINSAKEALKYG-DIVEFRIDLLNDVN---FKDIEEFSKIPSIITIRA 57 IC+P+++K A+ S+K ++ G DI+E RID + + + K++ + P I T R Sbjct: 10 ICVPILEKTYESALESSKSSINAGADILELRIDFIENSDPDAVKNLIQEINFPLIATNRR 69 Query: 58 EWEGGAWRKSNEERIELLKNAIKNNAKFIDIELKEE-KNLELVKYRNEIGSTTKIIVSYH 116 E G ++ S +RIE+L A K A+ +DIEL E NL + ++++ IVSYH Sbjct: 70 REENGFFKGSESDRIEILLEAAKV-AEIVDIELGTELDNLNKIVKKSKLA-----IVSYH 123 Query: 117 DFEKTPEIDELIDVVEKELKIGDIAKFATFAHSKEDTLKILNLMNRYSGKIIAIGMGESG 176 DFEKTP+ D L+++V KELK+GDIAKFA + DTL +LN+++ +AI MG+ G Sbjct: 124 DFEKTPDKDFLLEIVNKELKLGDIAKFAVMPKTMADTLIVLNVLSEVE-NTVAISMGDIG 182 Query: 177 KLTRILGLDFGSILTFASMGGKASAPGQVDVKKLKEIL 214 TR++ FGS LTFAS +SAPGQ++++ ++ + Sbjct: 183 SYTRVVAPLFGSPLTFASY-ENSSAPGQLNIETTRDFI 219 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: 136 Number of extensions: 11 Number of successful extensions: 4 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: 225 Length adjustment: 22 Effective length of query: 196 Effective length of database: 203 Effective search space: 39788 Effective search space used: 39788 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_013644232.1 METBO_RS03210 (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.2544.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-55 173.0 0.1 6e-55 172.8 0.1 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013644232.1 METBO_RS03210 type I 3-dehydroqu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013644232.1 METBO_RS03210 type I 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 172.8 0.1 6e-55 6e-55 2 228 .. 10 218 .. 9 219 .. 0.95 Alignments for each domain: == domain 1 score: 172.8 bits; conditional E-value: 6e-55 TIGR01093 2 ilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqke 70 i+vp+ +k+ e ale + + gaDi+ElR+D+ +++ + v+++++++ + pli T R+ +e lcl|NCBI__GCF_000191585.1:WP_013644232.1 10 ICVPILEKTYESALESSKSSINAGADILELRIDFIENSDPDA-VKNLIQEI-----NFPLIATNRRREE 72 9************************************99995.********.....6************ PP TIGR01093 71 GGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelv 139 G fkg+e +r+e l ea++ ++vDiEl +e + +++++k + + i+S+Hdfektp+k+ l lcl|NCBI__GCF_000191585.1:WP_013644232.1 73 NGFFKGSESDRIEILLEAAKVA--EIVDIELGTELDNLNKIVK----KSKLAIVSYHDFEKTPDKDFLL 135 ***************9988866..************9887766....6677899*************** PP TIGR01093 140 erlekaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltf 208 e+++k +l +Di+K+avm+k + D l +l+++ +ve + +a+sMg+ G+ +Rv++ ++gs ltf lcl|NCBI__GCF_000191585.1:WP_013644232.1 136 EIVNKELKL-GDIAKFAVMPKTMADTLIVLNVLSEVE-----NTVAISMGDIGSYTRVVAPLFGSPLTF 198 *********.**************************8.....9************************** PP TIGR01093 209 gslgkasAPGQisvkelrel 228 +s +++sAPGQ+++++ r + lcl|NCBI__GCF_000191585.1:WP_013644232.1 199 ASYENSSAPGQLNIETTRDF 218 **************998865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (225 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: 00:00:00.00 # Mc/sec: 8.92 // [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