Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 3608146 Dshi_1551 3-dehydroquinate dehydratase, type II (RefSeq)
Query= BRENDA::N1V364 (155 letters) >FitnessBrowser__Dino:3608146 Length = 150 Score = 168 bits (425), Expect = 4e-47 Identities = 79/134 (58%), Positives = 102/134 (76%) Query: 16 LLVLNGPNLNLLGTREPQIYGSDTLEDAETLAARAAEAHGLAVECLQSNHEGVLIDAIHA 75 + +LNGPNLNLLGTR+P++YG+ TL D E + R A+A GL +E Q+NHEGVLID IHA Sbjct: 3 ITILNGPNLNLLGTRQPEVYGATTLADIEHMCQRKAQALGLEIEFNQTNHEGVLIDQIHA 62 Query: 76 ARGTAAGIVINPGGYTHTSVALRDALSGVDLPVVEVHISNIHRREEFRHHSYISGIAVAV 135 AR + G++IN G YTHTSVAL DA++ V LP VEVH+SNIH RE FRH S++S +A+ + Sbjct: 63 ARSESDGLIINAGAYTHTSVALMDAVASVSLPTVEVHLSNIHARESFRHTSFLSPVALGL 122 Query: 136 IAGAGISGYKFAVD 149 I G G +GY A+D Sbjct: 123 ICGFGATGYVMALD 136 Lambda K H 0.317 0.133 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: 84 Number of extensions: 1 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: 155 Length of database: 150 Length adjustment: 17 Effective length of query: 138 Effective length of database: 133 Effective search space: 18354 Effective search space used: 18354 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 43 (21.2 bits)
Align candidate 3608146 Dshi_1551 (3-dehydroquinate dehydratase, type II (RefSeq))
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.5589.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-63 198.0 0.1 3e-63 197.8 0.1 1.0 1 lcl|FitnessBrowser__Dino:3608146 Dshi_1551 3-dehydroquinate dehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608146 Dshi_1551 3-dehydroquinate dehydratase, type II (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 197.8 0.1 3e-63 3e-63 1 139 [. 2 140 .. 2 142 .. 0.98 Alignments for each domain: == domain 1 score: 197.8 bits; conditional E-value: 3e-63 TIGR01088 1 kilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgivinpaalt 77 +i +lnGPnlnlLG+r+p+vyG++tl +ie++++++a++l++e+e+ q+n+eg lid+ih a + dg++in++a+t lcl|FitnessBrowser__Dino:3608146 2 HITILNGPNLNLLGTRQPEVYGATTLADIEHMCQRKAQALGLEIEFNQTNHEGVLIDQIHAARSESDGLIINAGAYT 78 589************************************************************************** PP TIGR01088 78 htsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealve 139 htsval Da+a+vslP+vevhlsn+hare+fr++s+l++va G i+G+Ga+gy +al + lcl|FitnessBrowser__Dino:3608146 79 HTSVALMDAVASVSLPTVEVHLSNIHARESFRHTSFLSPVALGLICGFGATGYVMALDGIWA 140 *********************************************************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (150 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: 4.86 // [ok]
This GapMind analysis is from Apr 09 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