Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_028999773.1 H537_RS0123300 type II 3-dehydroquinate dehydratase
Query= BRENDA::Q88IJ6 (145 letters) >NCBI__GCF_000430725.1:WP_028999773.1 Length = 148 Score = 218 bits (556), Expect = 2e-62 Identities = 104/141 (73%), Positives = 122/141 (86%) Query: 5 VLMLHGINHNMFGKRDPRQYGTATLADIDQALQALGEELGAQVESFQSNFEGAMCERIHQ 64 +L LHGIN NMFGKRDP+QYGTATLA ID L+ALG+ELGA+VE FQ+NFEG M ERIH+ Sbjct: 3 ILTLHGINLNMFGKRDPKQYGTATLAQIDDQLRALGQELGAEVECFQTNFEGEMAERIHR 62 Query: 65 AYEDRVDAVLINAGAWTHYSYGIRDALAIIEVPVVEVHMSNIHAREPFRHHSVFAEVVRG 124 A+ D +AV+INAGAWTHYSYGIRDALAI++ P++EVHMSNIHARE FRH SV AE+ RG Sbjct: 63 AHTDGTEAVIINAGAWTHYSYGIRDALAILKCPIIEVHMSNIHAREAFRHTSVIAELARG 122 Query: 125 QICGFGVETYLLALRAAMSMV 145 QI GFGV++YLL LRAA+S V Sbjct: 123 QIAGFGVDSYLLGLRAAVSAV 143 Lambda K H 0.324 0.136 0.404 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: 118 Number of extensions: 6 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: 145 Length of database: 148 Length adjustment: 16 Effective length of query: 129 Effective length of database: 132 Effective search space: 17028 Effective search space used: 17028 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 42 (20.8 bits)
Align candidate WP_028999773.1 H537_RS0123300 (type II 3-dehydroquinate dehydratase)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (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/TIGR01088.hmm # target sequence database: /tmp/gapView.10746.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01088 [M=141] Accession: TIGR01088 Description: aroQ: 3-dehydroquinate dehydratase, type II 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-58 180.7 0.1 6.3e-58 180.5 0.1 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028999773.1 H537_RS0123300 type II 3-dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028999773.1 H537_RS0123300 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.5 0.1 6.3e-58 6.3e-58 1 140 [. 2 142 .. 2 143 .. 0.98 Alignments for each domain: == domain 1 score: 180.5 bits; conditional E-value: 6.3e-58 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdg 68 kil l+G nln++Gkr+pk yG+ tl +i+++l++ ++el+ eve+fq+n+ege+ ++ih+a+ + ++ lcl|NCBI__GCF_000430725.1:WP_028999773.1 2 KILTLHGINLNMFGKRDPKQYGTATLAQIDDQLRALGQELGAEVECFQTNFEGEMAERIHRAHTDgTEA 70 6999**********************************************************98879** PP TIGR01088 69 ivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklaleal 137 ++in++a+th+s+ +rDala+++ P++evh+sn+hare fr++sv+ae a+G+i G+G+ +y l+l+a+ lcl|NCBI__GCF_000430725.1:WP_028999773.1 71 VIINAGAWTHYSYGIRDALAILKCPIIEVHMSNIHAREAFRHTSVIAELARGQIAGFGVDSYLLGLRAA 139 *******************************************************************99 PP TIGR01088 138 vea 140 v+a lcl|NCBI__GCF_000430725.1:WP_028999773.1 140 VSA 142 875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (148 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: 4.44 // [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