Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_084275691.1 B8779_RS06290 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_900176045.1:WP_084275691.1 Length = 167 Score = 192 bits (489), Expect = 2e-54 Identities = 92/164 (56%), Positives = 122/164 (74%), Gaps = 1/164 (0%) Query: 3 SIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKN 62 ++I G+VWKFG+N+DTD I+ ARYL + P ELA+ VM ADP+F KK++PGDIIV G+N Sbjct: 2 NVITGKVWKFGDNIDTDLIIAARYLNTSDPHELAKHVMEDADPEFVKKLQPGDIIVAGEN 61 Query: 63 FGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEV 122 FGCGSSREHAP+ LK AG++ V+A+SFARIFYRNA N+GLP+ E K ++K+NEGD + + Sbjct: 62 FGCGSSREHAPIALKAAGVAAVVAKSFARIFYRNAFNMGLPIFELKE-TDKINEGDLISI 120 Query: 123 NLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAE 166 ++E G IK+L +P FM E+L GGLM Y K K+ E Sbjct: 121 DMEKGVIKDLDKHNEYTFTPIPPFMQELLSCGGLMNYAKAKILE 164 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: 121 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: 167 Length adjustment: 18 Effective length of query: 150 Effective length of database: 149 Effective search space: 22350 Effective search space used: 22350 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_084275691.1 B8779_RS06290 (3-isopropylmalate dehydratase small subunit)
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.1537205.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-70 221.3 0.0 2.9e-70 221.1 0.0 1.0 1 NCBI__GCF_900176045.1:WP_084275691.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900176045.1:WP_084275691.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.1 0.0 2.9e-70 2.9e-70 1 155 [. 6 159 .. 6 161 .. 0.99 Alignments for each domain: == domain 1 score: 221.1 bits; conditional E-value: 2.9e-70 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaalalkaa 73 G+vwkfGd++dtd ii +ryl t d++elakh+me++dpef kk ++Gd+ivaG+nfG+Gssre+a++alkaa NCBI__GCF_900176045.1:WP_084275691.1 6 GKVWKFGDNIDTDLIIAARYLNTSDPHELAKHVMEDADPEFVKKLQPGDIIVAGENFGCGSSREHAPIALKAA 78 9************************************************************************ PP TIGR02087 74 GvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleeledllleile 146 Gvaav+a+sfarifyrna n+Glp+ +++ t++i++Gd +++d+ekg i+ + k++++++ +++ ++ e+l+ NCBI__GCF_900176045.1:WP_084275691.1 79 GVAAVVAKSFARIFYRNAFNMGLPIFELK-ETDKINEGDLISIDMEKGVIKDLDKHNEYTFTPIPPFMQELLS 150 **************************999.78***************************************** PP TIGR02087 147 eGGlleylk 155 GGl++y k NCBI__GCF_900176045.1:WP_084275691.1 151 CGGLMNYAK 159 *******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (167 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: 14.80 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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