Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_017547915.1 C792_RS0102765 type I 3-dehydroquinate dehydratase
Query= BRENDA::P36923 (253 letters) >NCBI__GCF_000330705.1:WP_017547915.1 Length = 253 Score = 160 bits (404), Expect = 3e-44 Identities = 88/248 (35%), Positives = 140/248 (56%), Gaps = 4/248 (1%) Query: 6 VKNVRIGEGNPKIVVPIVAPTAEDILAEATASQTLD--CDLVEWRLDYYENVADFSDVCN 63 +K+V IGEG PK+VV T E+I AE ++T D+VE R D ++ + + D Sbjct: 3 IKDVTIGEGQPKVVVSFTGHTPEEIRAEIAEARTNSDKFDIVEIRSDSFDAM-NHEDHFA 61 Query: 64 LSQQVMERLGQKPLLLTFRTQKEGGEMAFSEENYFALYHELVKKGALDLLDIELFANPLA 123 + + +G P++ T+RT EGG S Y +L + +D++DIE F Sbjct: 62 VVDHISREMGDYPIIYTYRTNGEGGNGTKSAAEYQSLLSHAIDHSEIDIVDIEFFMYEEI 121 Query: 124 ADTLIHEAKKAGIKIVLCNHDFQKTPSQEEIVARLRQMQMRQADICKIAVMPQDATDVLT 183 D L+ AK+ G+ ++L HDF+ TP E+++A + M R DI K+A P D DVL+ Sbjct: 122 VDQLVARAKEKGVAVLLSQHDFRDTPHFEDMMATYKNMYERGGDILKLAYQPADGRDVLS 181 Query: 184 LLSATNEMYTHYASVPIVTMSMGQLGMISRVTGQLFGSALTFGSAQQASAPGQLSVQVLR 243 +LSA ++ + + +V ++MG+ G I+RV G +FGS LT+G +APGQ++ +L+ Sbjct: 182 VLSAVHDARRKF-NCQVVGIAMGEAGKITRVAGGVFGSCLTYGHLVNQAAPGQINAGILK 240 Query: 244 NYLKTFEQ 251 YL FE+ Sbjct: 241 EYLNIFEE 248 Lambda K H 0.319 0.133 0.374 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: 139 Number of extensions: 9 Number of successful extensions: 3 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: 253 Length of database: 253 Length adjustment: 24 Effective length of query: 229 Effective length of database: 229 Effective search space: 52441 Effective search space used: 52441 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_017547915.1 C792_RS0102765 (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.3486334.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-60 189.7 0.0 4.6e-60 189.5 0.0 1.0 1 NCBI__GCF_000330705.1:WP_017547915.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017547915.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 189.5 0.0 4.6e-60 4.6e-60 2 228 .. 15 242 .. 14 243 .. 0.93 Alignments for each domain: == domain 1 score: 189.5 bits; conditional E-value: 4.6e-60 TIGR01093 2 ilvpltakdleealeelekik..evgaDivElRvDllkdvsseksveavaeqlsellkdlplilTiRtqkeGG 72 ++v+ t ++ ee+ +e+ +++ +DivE+R D+++ +++e+ av++++s + d+p+i T+Rt+ eGG NCBI__GCF_000330705.1:WP_017547915.1 15 VVVSFTGHTPEEIRAEIAEARtnSDKFDIVEIRSDSFDAMNHED-HFAVVDHISREMGDYPIIYTYRTNGEGG 86 567777777777777666665323569***********999985.88999999999***************** PP TIGR01093 73 kfkgdeeerleelkeaieknlvdlvDiElkleeeavkelikeakkaktkiilSnHdfektpskeelverleka 145 + +++ e+ +l++ai+++ +d+vDiE ++ ee+v++l++ ak++++ ++lS+Hdf+ tp e++++ ++++ NCBI__GCF_000330705.1:WP_017547915.1 87 NGTKSAAEYQSLLSHAIDHSEIDIVDIEFFMYEEIVDQLVARAKEKGVAVLLSQHDFRDTPHFEDMMATYKNM 159 ************************************************************************* PP TIGR01093 146 qsldaDivKiavmaksieDvltLleitlkveeekdkplialsMgekGkisRvlgavlgsvltfgslgkasAPG 218 ++ ++Di+K+a + + +Dvl +l++ ++++ + +++++ Mge Gki+Rv+g v+gs lt+g+l +++APG NCBI__GCF_000330705.1:WP_017547915.1 160 YERGGDILKLAYQPADGRDVLSVLSAVHDARRKFNCQVVGIAMGEAGKITRVAGGVFGSCLTYGHLVNQAAPG 232 ******************************9888*************************************** PP TIGR01093 219 Qisvkelrel 228 Qi+ l+e+ NCBI__GCF_000330705.1:WP_017547915.1 233 QINAGILKEY 242 **99988886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (229 nodes) Target sequences: 1 (253 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.15 // [ok]
This GapMind analysis is from Jul 26 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