Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_073038273.1 BUB04_RS06995 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_900129305.1:WP_073038273.1 Length = 172 Score = 188 bits (477), Expect = 5e-53 Identities = 86/165 (52%), Positives = 118/165 (71%) Query: 1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGG 60 M+ I++GR FGNN+DTD I P +YL EE+ + M G DP F K +PGDIIVGG Sbjct: 1 MKRILEGRAHVFGNNLDTDQIYPGQYLELVTAEEIGRHAMEGVDPRFVKNFRPGDIIVGG 60 Query: 61 KNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDEL 120 NFGCGSSREHA + L+ G ++AESFARIFYRNA+N+GLP++ C G+S +V+ GD L Sbjct: 61 TNFGCGSSREHAAIALRAVGAGGIVAESFARIFYRNAVNLGLPVLVCPGVSRRVSSGDRL 120 Query: 121 EVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165 V+LE G ++N TTG ++ + L E + EILE+GG+ P +K+++A Sbjct: 121 VVDLEKGRVRNATTGVEMEAEPLTEVVFEILESGGIKPLVKRQLA 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: 116 Number of extensions: 5 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: 172 Length adjustment: 18 Effective length of query: 150 Effective length of database: 154 Effective search space: 23100 Effective search space used: 23100 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_073038273.1 BUB04_RS06995 (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.740.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-60 189.0 0.0 2.5e-60 188.9 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073038273.1 BUB04_RS06995 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900129305.1:WP_073038273.1 BUB04_RS06995 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.9 0.0 2.5e-60 2.5e-60 1 156 [. 7 162 .. 7 163 .. 0.98 Alignments for each domain: == domain 1 score: 188.9 bits; conditional E-value: 2.5e-60 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 Gr++ fG+++dtd+i Pg+yl ++ +e+++hameg+dp f k+ r+Gd+iv G nfG+Gssre+aa+a lcl|NCBI__GCF_900129305.1:WP_073038273.1 7 GRAHVFGNNLDTDQIYPGQYLELVTAEEIGRHAMEGVDPRFVKNFRPGDIIVGGTNFGCGSSREHAAIA 75 9******************************************************************** PP TIGR02087 70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138 l+a+G +++aesfarifyrna+n Glp++v +v + Gd++ vdlekg++r+ + +++ e+l+ lcl|NCBI__GCF_900129305.1:WP_073038273.1 76 LRAVGAGGIVAESFARIFYRNAVNLGLPVLVCPGVSRRVSSGDRLVVDLEKGRVRNATTGVEMEAEPLT 144 ********************************************************************* PP TIGR02087 139 dllleileeGGlleylkk 156 +++ eile+GG+ ++k+ lcl|NCBI__GCF_900129305.1:WP_073038273.1 145 EVVFEILESGGIKPLVKR 162 ************988887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (172 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: 5.52 // [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