Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_013518871.1 ALIDE2_RS11385 type II 3-dehydroquinate dehydratase
Query= BRENDA::P15474 (157 letters) >NCBI__GCF_000204645.1:WP_013518871.1 Length = 149 Score = 166 bits (420), Expect = 2e-46 Identities = 81/143 (56%), Positives = 102/143 (71%), Gaps = 6/143 (4%) Query: 10 IMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHE 69 + +LNGPNLNLLG R+P++YGS TLADVE +C A HG + FRQSNHEG LVDWIHE Sbjct: 6 VYVLNGPNLNLLGTREPQVYGSQTLADVEQICAAACTRHGLALVFRQSNHEGALVDWIHE 65 Query: 70 ARLNH-----CGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVS 124 A H G+V+N AAY+HTSVA+LDA+ G+P+VE+HISN+H RE FRH SY++ Sbjct: 66 AGRLHAEGKLAGVVLNAAAYTHTSVALLDAVKG-TGVPLVELHISNVHARESFRHRSYLA 124 Query: 125 QRADGVVAGCGVQGYVFGVERIA 147 A V+ G GVQGY + +A Sbjct: 125 GAARAVMCGFGVQGYALAIAGVA 147 Lambda K H 0.320 0.135 0.411 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: 111 Number of extensions: 4 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: 157 Length of database: 149 Length adjustment: 17 Effective length of query: 140 Effective length of database: 132 Effective search space: 18480 Effective search space used: 18480 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: 43 (21.2 bits)
Align candidate WP_013518871.1 ALIDE2_RS11385 (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.13344.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-58 180.2 0.1 9.3e-58 180.0 0.1 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013518871.1 ALIDE2_RS11385 type II 3-dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013518871.1 ALIDE2_RS11385 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 180.0 0.1 9.3e-58 9.3e-58 2 138 .. 6 147 .. 5 149 .] 0.95 Alignments for each domain: == domain 1 score: 180.0 bits; conditional E-value: 9.3e-58 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihea.....leq 65 + vlnGPnlnlLG+rep+vyGs+tl ++e+++ +a +++++ + ++qsn+eg l+d+ihea +++ lcl|NCBI__GCF_000204645.1:WP_013518871.1 6 VYVLNGPNLNLLGTREPQVYGSQTLADVEQICAAACTRHGLALVFRQSNHEGALVDWIHEAgrlhaEGK 74 78*********************************************************9633333788 PP TIGR01088 66 vdgivinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklal 134 + g+v+n+aa+thtsval Da++ +P+ve+h+snvhare+fr++s+la +a+ v++G+G++gy la+ lcl|NCBI__GCF_000204645.1:WP_013518871.1 75 LAGVVLNAAAYTHTSVALLDAVKGTGVPLVELHISNVHARESFRHRSYLAGAARAVMCGFGVQGYALAI 143 9*******************************************************************9 PP TIGR01088 135 ealv 138 ++ lcl|NCBI__GCF_000204645.1:WP_013518871.1 144 AGVA 147 8776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (149 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: 4.91 // [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