Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate Ga0059261_0290 Ga0059261_0290 3-dehydroquinate dehydratase (EC 4.2.1.10)
Query= BRENDA::A0A124C1Y7 (157 letters) >FitnessBrowser__Korea:Ga0059261_0290 Length = 144 Score = 152 bits (383), Expect = 3e-42 Identities = 77/141 (54%), Positives = 95/141 (67%), Gaps = 2/141 (1%) Query: 10 IMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAATHGGTVDFRQSNHEGELVDWIHE 69 I +LNGPNLNLLG R+PEIYGSDTL D+ + G T+D RQSNHEG L+DW+HE Sbjct: 5 IYVLNGPNLNLLGMREPEIYGSDTLDDIAGMLEDRGRELGLTIDMRQSNHEGHLIDWMHE 64 Query: 70 AR-MDHCGIVINPGAYSHTSVAILDALNTCDGLPVIEVHISNIHKREAFRHHSYVSLRAD 128 A+ D I++N GAY+HTS+A+ D + + PVIEVHISN H RE +R HSYV + A Sbjct: 65 AQARDAKAILLNSGAYTHTSLALYDCIRSI-RTPVIEVHISNPHAREEYRRHSYVGMAAK 123 Query: 129 GVIAGCGVQGYVFGVERVAAL 149 G IAG G YV +E A L Sbjct: 124 GTIAGFGALSYVLALEAAARL 144 Lambda K H 0.321 0.137 0.416 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: 96 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: 144 Length adjustment: 16 Effective length of query: 141 Effective length of database: 128 Effective search space: 18048 Effective search space used: 18048 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: 42 (20.8 bits)
Align candidate Ga0059261_0290 Ga0059261_0290 (3-dehydroquinate dehydratase (EC 4.2.1.10))
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.9458.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-57 179.6 0.0 1.4e-57 179.4 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0290 Ga0059261_0290 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0290 Ga0059261_0290 3-dehydroquinate dehydratase (EC 4.2.1.10) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 179.4 0.0 1.4e-57 1.4e-57 2 138 .. 5 142 .. 4 144 .] 0.98 Alignments for each domain: == domain 1 score: 179.4 bits; conditional E-value: 1.4e-57 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeq.vdgi 69 i vlnGPnlnlLG rep++yGs tl++i +le+ ++el++ ++++qsn+eg+lid++hea+ + +++i lcl|FitnessBrowser__Korea:Ga0059261_0290 5 IYVLNGPNLNLLGMREPEIYGSDTLDDIAGMLEDRGRELGLTIDMRQSNHEGHLIDWMHEAQARdAKAI 73 88***********************************************************98879*** PP TIGR01088 70 vinpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealv 138 ++n++a+thts+al D + +++ Pv+evh+sn haree+r++s+++ +akG+i G+Ga +y lalea++ lcl|FitnessBrowser__Korea:Ga0059261_0290 74 LLNSGAYTHTSLALYDCIRSIRTPVIEVHISNPHAREEYRRHSYVGMAAKGTIAGFGALSYVLALEAAA 142 *****************************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (144 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: 4.84 // [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