Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_007473885.1 CMTB2_RS02915 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_000170735.1:WP_007473885.1 Length = 169 Score = 196 bits (498), Expect = 2e-55 Identities = 96/165 (58%), Positives = 126/165 (76%), Gaps = 1/165 (0%) Query: 3 SIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKN 62 +II GRVWKFG+N+DTD I+PARYL + P ELA+ VM ADP+FPKKV+PGDIIV G N Sbjct: 2 NIITGRVWKFGDNIDTDLIIPARYLNTSDPHELAKHVMEDADPEFPKKVRPGDIIVAGYN 61 Query: 63 FGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEV 122 FG GSSREHAP+ LK AGIS VIA+SFARIFYRN+ N+GLP+ E S+++NEGD +++ Sbjct: 62 FGSGSSREHAPIALKAAGISAVIAKSFARIFYRNSFNMGLPIFELLE-SDEINEGDLIKI 120 Query: 123 NLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAES 167 +L+ G I N+ TG+ K +P FM ++ AGGL+ Y K+ + E+ Sbjct: 121 DLDKGIIHNVDTGKNYKFAPIPPFMQNLIAAGGLINYAKEILKEN 165 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: 131 Number of extensions: 4 Number of successful extensions: 2 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: 169 Length adjustment: 18 Effective length of query: 150 Effective length of database: 151 Effective search space: 22650 Effective search space used: 22650 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 WP_007473885.1 CMTB2_RS02915 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR02084 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))
# 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/TIGR02084.hmm # target sequence database: /tmp/gapView.9036.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02084 [M=156] Accession: TIGR02084 Description: leud: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-79 249.4 0.0 6e-79 249.3 0.0 1.0 1 lcl|NCBI__GCF_000170735.1:WP_007473885.1 CMTB2_RS02915 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000170735.1:WP_007473885.1 CMTB2_RS02915 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.3 0.0 6e-79 6e-79 1 156 [] 6 160 .. 6 160 .. 0.99 Alignments for each domain: == domain 1 score: 249.3 bits; conditional E-value: 6e-79 TIGR02084 1 gkvlkygdnvdtdviiparylntsdpkelakhcmedldkefkkkvkegdilvagknfgcgssrehapia 69 g+v+k+gdn+dtd iiparylntsdp+elakh+med+d ef kkv+ gdi+vag nfg+gssrehapia lcl|NCBI__GCF_000170735.1:WP_007473885.1 6 GRVWKFGDNIDTDLIIPARYLNTSDPHELAKHVMEDADPEFPKKVRPGDIIVAGYNFGSGSSREHAPIA 74 89******************************************************************* PP TIGR02084 70 ikasgiscviaksfarifyrnainiglpiveseeavdeleegdevevdlekgiiknvkkgkeykakpfp 138 +ka+gis+viaksfarifyrn+ n+glpi e+ e+ de++egd +++dl+kgii+nv +gk+yk p p lcl|NCBI__GCF_000170735.1:WP_007473885.1 75 LKAAGISAVIAKSFARIFYRNSFNMGLPIFELLES-DEINEGDLIKIDLDKGIIHNVDTGKNYKFAPIP 142 **********************************9.********************************* PP TIGR02084 139 eflkeilkaegllnyvkk 156 +f+++++ a+gl+ny+k+ lcl|NCBI__GCF_000170735.1:WP_007473885.1 143 PFMQNLIAAGGLINYAKE 160 ***************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 1 (169 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: 4.43 // [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