Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate 8501057 DvMF_1793 3-isopropylmalate dehydratase, small subunit (RefSeq)
Query= BRENDA::Q58673 (168 letters) >FitnessBrowser__Miya:8501057 Length = 163 Score = 167 bits (423), Expect = 8e-47 Identities = 81/159 (50%), Positives = 112/159 (70%) Query: 7 GRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCG 66 G K G ++DTDAI+PAR+LV T ++L + M G + + K+VKPGD++V G+NFGCG Sbjct: 5 GTAHKVGEHIDTDAIIPARFLVTTDTQKLGENCMAGLEEGWVKRVKPGDVMVAGRNFGCG 64 Query: 67 SSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLET 126 SSREHAP+ + GAG+ VIA SFARIFYRNA N+GL L+E +K+ +GD +EV+ Sbjct: 65 SSREHAPIAILGAGMPVVIAHSFARIFYRNAFNMGLLLLEVGDEVDKIADGDTVEVDAAK 124 Query: 127 GEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165 G I N TTG + LP M E+L+ GGL+PY+++K+A Sbjct: 125 GLITNRTTGATITCPPLPASMRELLDKGGLVPYVREKLA 163 Lambda K H 0.317 0.139 0.405 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: 110 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: 168 Length of database: 163 Length adjustment: 18 Effective length of query: 150 Effective length of database: 145 Effective search space: 21750 Effective search space used: 21750 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 8501057 DvMF_1793 (3-isopropylmalate dehydratase, small subunit (RefSeq))
to HMM TIGR02087 (3-isopropylmalate dehydratase, small subunit)
# 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/TIGR02087.hmm # target sequence database: /tmp/gapView.3605.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02087 [M=157] Accession: TIGR02087 Description: LEUD_arch: 3-isopropylmalate dehydratase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-57 178.6 0.0 4.2e-57 178.4 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501057 DvMF_1793 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501057 DvMF_1793 3-isopropylmalate dehydratase, small subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 178.4 0.0 4.2e-57 4.2e-57 1 156 [. 5 160 .. 5 161 .. 0.98 Alignments for each domain: == domain 1 score: 178.4 bits; conditional E-value: 4.2e-57 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaalalkaaGvaa 77 G ++k G+++dtdaiiP+r+l ttd+++l++ +m+g+++ + k+v++Gdv+vaG+nfG+Gssre+a++a+ aG+ lcl|FitnessBrowser__Miya:8501057 5 GTAHKVGEHIDTDAIIPARFLVTTDTQKLGENCMAGLEEGWVKRVKPGDVMVAGRNFGCGSSREHAPIAILGAGMPV 81 789************************************************************************** PP TIGR02087 78 viaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleeledllleileeGGlleyl 154 via+sfarifyrna n+Gl l+++ d +++i dGd+vevd kg i + + ++++ +l+ ++e+l++GGl+ y+ lcl|FitnessBrowser__Miya:8501057 82 VIAHSFARIFYRNAFNMGLLLLEVGDEVDKIADGDTVEVDAAKGLITNRTTGATITCPPLPASMRELLDKGGLVPYV 158 ****************************************************************************9 PP TIGR02087 155 kk 156 + lcl|FitnessBrowser__Miya:8501057 159 RE 160 85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (163 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.58 // [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