Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_041675826.1 SULAZ_RS04400 type I 3-dehydroquinate dehydratase
Query= curated2:B4U701 (217 letters) >NCBI__GCF_000021545.1:WP_041675826.1 Length = 242 Score = 162 bits (409), Expect = 7e-45 Identities = 91/223 (40%), Positives = 139/223 (62%), Gaps = 6/223 (2%) Query: 1 MKIAIPITDENFDEVLLKA--RNADILEFRVDSFTNKDISFVSGLLKKAKENGFETILTI 58 +KIA+PI DEN + L A N DI+E R+D F +KD++ + G++KK KE GF + T+ Sbjct: 14 VKIAVPIIDENVENTLSIALLENVDIIELRIDQFKSKDLAHILGIIKKVKEKGFIALATV 73 Query: 59 RSEKEGGAYV--ENRVEMFEKLMPLSDYTDIELSSTDIIAYISRLSKEYNKKLIVSYHNF 116 RS+ EGGA + E R+++F + D DIE +S I I L K +I+SYH+F Sbjct: 74 RSKLEGGADIPDEERLKIFSSIADYVDMVDIEYTSFRINKEIVDLYHSKGKAVIMSYHDF 133 Query: 117 EMTPANFVIKETIREALRYG-DIPKIALKANSYEDVARLMCSAIDIKTPKIL-ISMGEFG 174 E TP++ I+ I E+ G DI K A KANS++DVAR+MC + ++ I MGE G Sbjct: 134 EKTPSDDYIQSIIDESKTLGADIVKYAFKANSFQDVARVMCITHRNREKNLVAILMGEIG 193 Query: 175 KISRIAGFIFGSFISYAYLEKPNAPGQLSLEEMLKLKEMFYLR 217 K+SR+ +FGS I+Y ++ + APGQ+ ++++ +L E F ++ Sbjct: 194 KVSRVVAPVFGSLITYTFIGQSFAPGQIEVQKLNELLEFFNIQ 236 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: 148 Number of extensions: 10 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: 242 Length adjustment: 23 Effective length of query: 194 Effective length of database: 219 Effective search space: 42486 Effective search space used: 42486 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_041675826.1 SULAZ_RS04400 (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.9039.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-54 170.5 1.0 3.7e-54 170.2 1.0 1.0 1 lcl|NCBI__GCF_000021545.1:WP_041675826.1 SULAZ_RS04400 type I 3-dehydroqu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_041675826.1 SULAZ_RS04400 type I 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.2 1.0 3.7e-54 3.7e-54 1 229 [] 15 230 .. 15 230 .. 0.91 Alignments for each domain: == domain 1 score: 170.2 bits; conditional E-value: 3.7e-54 TIGR01093 1 kilvpltakdleealeelekikevgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqk 69 ki+vp+ ++++e+ l+ + ++Di+ElR+D++k + + ++++++ k + T+R++ lcl|NCBI__GCF_000021545.1:WP_041675826.1 15 KIAVPIIDENVENTLSIALL---ENVDIIELRIDQFKSKDLAH-ILGIIKKVK--EKGFIALATVRSKL 77 699**********9999887...469***********988885.888888884..47788899****** PP TIGR01093 70 eGGkfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeel 138 eGG + +eerl+ + +++ vd+vDiE ++ ke++ + +++ +i+S+Hdfektps + + lcl|NCBI__GCF_000021545.1:WP_041675826.1 78 EGGA-DIPDEERLKIFSSIADY--VDMVDIEYTSFRI-NKEIVDLYHSKGKAVIMSYHDFEKTPSDDYI 142 ***6.67788999999777765..6******987654.678999999********************** PP TIGR01093 139 verlekaqsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvlt 207 ++++ + ++l+aDivK a +a+s++Dv+++++it + + +k+l+a+ Mge Gk+sRv++ v+gs +t lcl|NCBI__GCF_000021545.1:WP_041675826.1 143 QSIIDESKTLGADIVKYAFKANSFQDVARVMCITHRNR---EKNLVAILMGEIGKVSRVVAPVFGSLIT 208 **********************************7776...9*************************** PP TIGR01093 208 fgslgkasAPGQisvkelrell 229 + +g+++APGQi+v++l+ell lcl|NCBI__GCF_000021545.1:WP_041675826.1 209 YTFIGQSFAPGQIEVQKLNELL 230 *******************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (242 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: 8.51 // [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