Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate RR42_RS21080 RR42_RS21080 3-isopropylmalate dehydratase
Query= BRENDA::Q58673 (168 letters) >FitnessBrowser__Cup4G11:RR42_RS21080 Length = 170 Score = 140 bits (352), Expect = 1e-38 Identities = 72/160 (45%), Positives = 105/160 (65%), Gaps = 5/160 (3%) Query: 7 GRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGCG 66 GR+W+FG+NVDTD + P ++ EE+A+ + G P+FP V+PGD++V G+NFG G Sbjct: 12 GRIWRFGDNVDTDQMAPGTHMK-GGVEEIARHCLAGLRPEFPAAVRPGDLLVAGRNFGVG 70 Query: 67 SSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLET 126 SSRE AP L+ G++ VIA SFA +FYRNAIN+GLP++ C + V D LE Sbjct: 71 SSREQAPQALRHLGLAAVIAPSFAGLFYRNAINLGLPVLVCHDATRLV---DGAAARLEL 127 Query: 127 GE-IKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMA 165 G+ L G + + +PEF+ +L+AGGL+P+LK ++A Sbjct: 128 GQACLVLPDGSRVACEPIPEFLHALLQAGGLVPHLKARLA 167 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: 101 Number of extensions: 3 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: 168 Length of database: 170 Length adjustment: 18 Effective length of query: 150 Effective length of database: 152 Effective search space: 22800 Effective search space used: 22800 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 RR42_RS21080 RR42_RS21080 (3-isopropylmalate dehydratase)
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.24021.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-54 169.9 0.0 1.9e-54 169.8 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS21080 RR42_RS21080 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS21080 RR42_RS21080 3-isopropylmalate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.8 0.0 1.9e-54 1.9e-54 1 156 [. 12 164 .. 12 165 .. 0.97 Alignments for each domain: == domain 1 score: 169.8 bits; conditional E-value: 1.9e-54 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 Gr+w+fGd+vdtd++ Pg + + ++e+a+h+++g++pef+ vr+Gd++vaG+nfG+Gssreqa+ a lcl|FitnessBrowser__Cup4G11:RR42_RS21080 12 GRIWRFGDNVDTDQMAPGTHM-KGGVEEIARHCLAGLRPEFPAAVRPGDLLVAGRNFGVGSSREQAPQA 79 9******************99.5789******************************************* PP TIGR02087 70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138 l+++G+aavia sfa +fyrnain Glp++v +d+t l+ dG +++l + ++ +++ + + +e+++ lcl|FitnessBrowser__Cup4G11:RR42_RS21080 80 LRHLGLAAVIAPSFAGLFYRNAINLGLPVLVCHDATRLV-DGAAARLELGQACLV-LPDGSRVACEPIP 146 ***********************************9999.7************99.8************ PP TIGR02087 139 dllleileeGGlleylkk 156 ++l +l++GGl+ +lk lcl|FitnessBrowser__Cup4G11:RR42_RS21080 147 EFLHALLQAGGLVPHLKA 164 **************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (170 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: 7.54 // [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