Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_028949847.1 Q385_RS0100825 type I 3-dehydroquinate dehydratase
Query= curated2:B4U701 (217 letters) >NCBI__GCF_000619805.1:WP_028949847.1 Length = 230 Score = 155 bits (392), Expect = 6e-43 Identities = 88/223 (39%), Positives = 135/223 (60%), Gaps = 6/223 (2%) Query: 1 MKIAIPITDENFDEVLLKA--RNADILEFRVDSFTNKDISFVSGLLKKAKENGFETILTI 58 +K+A+PITD+N ++ L KA + DI+E R+D F +D + ++KK KE GF + T+ Sbjct: 2 VKLALPITDDNVEDTLSKALLEDIDIIELRIDQFKIRDFKHILDVIKKVKEKGFIALATV 61 Query: 59 RSEKEGGAYV--ENRVEMFEKLMPLSDYTDIELSSTDIIAYISRLSKEYNKKLIVSYHNF 116 RS+ EGGA + E R E+F ++ D DIE +S I + K +I+SYH+F Sbjct: 62 RSKLEGGADIPDEGRFEIFSQIADYVDMADIEYTSFKINKQVIDFYHSKGKSVIMSYHDF 121 Query: 117 EMTPANFVIKETIREALRYG-DIPKIALKANSYEDVARLMCSAIDIKTPKIL-ISMGEFG 174 E TP++ I+ I E+ G DI K A KA S+EDVAR+MC + ++ I MGE G Sbjct: 122 EKTPSDDYIQTIINESKLMGADIVKYAFKARSFEDVARVMCITHKNREKNLVAILMGEIG 181 Query: 175 KISRIAGFIFGSFISYAYLEKPNAPGQLSLEEMLKLKEMFYLR 217 K+SR+ +FGS I+Y ++ + APGQL +++ +L E F ++ Sbjct: 182 KVSRVIAPVFGSLITYTFIGQSFAPGQLEAKKLNELLEFFNIQ 224 Lambda K H 0.320 0.137 0.375 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: 147 Number of extensions: 9 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: 217 Length of database: 230 Length adjustment: 22 Effective length of query: 195 Effective length of database: 208 Effective search space: 40560 Effective search space used: 40560 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: 46 (22.3 bits)
Align candidate WP_028949847.1 Q385_RS0100825 (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.2251245.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-52 165.5 0.7 1.2e-52 165.3 0.7 1.0 1 NCBI__GCF_000619805.1:WP_028949847.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028949847.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 165.3 0.7 1.2e-52 1.2e-52 2 229 .] 4 218 .. 3 218 .. 0.91 Alignments for each domain: == domain 1 score: 165.3 bits; conditional E-value: 1.2e-52 TIGR01093 2 ilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGGkf 74 ++p+t++++e+ l+++ + Di+ElR+D++k + ++ v+++++ k + T+R++ eGG NCBI__GCF_000619805.1:WP_028949847.1 4 LALPITDDNVEDTLSKALL---EDIDIIELRIDQFKIRDFK-HILDVIKKVK--EKGFIALATVRSKLEGGA- 69 6789999999999998877...79***********976555.6889999994..57788899*********6. PP TIGR01093 75 kgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverlekaqs 147 + +e r+e +++++ vd+ DiE ++ + k++i + +++ +i+S+Hdfektps + ++ ++++ + NCBI__GCF_000619805.1:WP_028949847.1 70 DIPDEGRFEIFSQIADY--VDMADIEYTSFKI-NKQVIDFYHSKGKSVIMSYHDFEKTPSDDYIQTIINESKL 139 6778899****888875..5******988765.6789999********************************* PP TIGR01093 148 ldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPGQi 220 ++aDivK a +a+s+eDv+++++it k + +k+l+a+ Mge Gk+sRv++ v+gs +t+ +g+++APGQ+ NCBI__GCF_000619805.1:WP_028949847.1 140 MGADIVKYAFKARSFEDVARVMCITHKNR---EKNLVAILMGEIGKVSRVIAPVFGSLITYTFIGQSFAPGQL 209 *************************7776...9**************************************** PP TIGR01093 221 svkelrell 229 + k+l+ell NCBI__GCF_000619805.1:WP_028949847.1 210 EAKKLNELL 218 ******985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (230 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: 15.28 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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