Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_093393430.1 BM091_RS03265 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_900114975.1:WP_093393430.1 Length = 171 Score = 212 bits (540), Expect = 2e-60 Identities = 99/163 (60%), Positives = 126/163 (77%) Query: 6 KGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFGC 65 +GRVWKFGN++DTDAI+PARYL P ELA M AD DF KKV+PGDIIV GKNFGC Sbjct: 4 RGRVWKFGNDIDTDAIIPARYLNTHDPRELALHCMEDADADFAKKVQPGDIIVAGKNFGC 63 Query: 66 GSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNLE 125 GSSREHAP+ +K AG+SCVIA SFARIFYRNA N+GLP++EC + E V +G+ L V+L Sbjct: 64 GSSREHAPIAIKAAGVSCVIAASFARIFYRNAFNMGLPILECADLVEVVEDGEILSVDLS 123 Query: 126 TGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAESQ 168 +GEI +TG+ + Q +P FM E++EAGGL+PY+ +KM + + Sbjct: 124 SGEIIRESTGQTFRAQPVPPFMQELIEAGGLIPYVVQKMKKEE 166 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: 135 Number of extensions: 3 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: 171 Length adjustment: 18 Effective length of query: 150 Effective length of database: 153 Effective search space: 22950 Effective search space used: 22950 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_093393430.1 BM091_RS03265 (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.21882.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-70 219.5 0.0 1.1e-69 219.2 0.0 1.0 1 lcl|NCBI__GCF_900114975.1:WP_093393430.1 BM091_RS03265 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900114975.1:WP_093393430.1 BM091_RS03265 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.2 0.0 1.1e-69 1.1e-69 1 155 [. 5 159 .. 5 162 .. 0.98 Alignments for each domain: == domain 1 score: 219.2 bits; conditional E-value: 1.1e-69 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 GrvwkfG+d+dtdaiiP+ryl t d++ela h+me++d +fakkv++Gd+ivaGknfG+Gssre+a++a lcl|NCBI__GCF_900114975.1:WP_093393430.1 5 GRVWKFGNDIDTDAIIPARYLNTHDPRELALHCMEDADADFAKKVQPGDIIVAGKNFGCGSSREHAPIA 73 9******************************************************************** PP TIGR02087 70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138 +kaaGv +via sfarifyrna n+Glp+++ +d +e+++dG++++vdl++gei++ + ++++ ++++ lcl|NCBI__GCF_900114975.1:WP_093393430.1 74 IKAAGVSCVIAASFARIFYRNAFNMGLPILECADLVEVVEDGEILSVDLSSGEIIRESTGQTFRAQPVP 142 *******************************************************999*********** PP TIGR02087 139 dllleileeGGlleylk 155 ++ e++e+GGl+ y+ lcl|NCBI__GCF_900114975.1:WP_093393430.1 143 PFMQELIEAGGLIPYVV 159 *************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (171 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: 5.75 // [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