Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_027180538.1 G496_RS0118210 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_000429985.1:WP_027180538.1 Length = 166 Score = 183 bits (464), Expect = 1e-51 Identities = 90/162 (55%), Positives = 118/162 (72%) Query: 5 IKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNFG 64 IKG V K G ++DTDAI+PAR+LV T PEEL M G + + K+VK DI+V +NFG Sbjct: 3 IKGNVHKVGAHIDTDAIIPARFLVTTDPEELGANCMEGLEHGWIKRVKKNDIMVADENFG 62 Query: 65 CGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVNL 124 CGSSREHAP+ + GAGI V+A SFARIFYRN N+GL L+E K+++GDELEV+ Sbjct: 63 CGSSREHAPISILGAGIPVVVAHSFARIFYRNGFNMGLILLEVGDNVSKISDGDELEVDA 122 Query: 125 ETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKMAE 166 + GEIKN+TTGE + +P FM EIL +GGL+ Y+KK+++E Sbjct: 123 DKGEIKNITTGETITCNPVPPFMKEILNSGGLVEYVKKRLSE 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: 123 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: 166 Length adjustment: 18 Effective length of query: 150 Effective length of database: 148 Effective search space: 22200 Effective search space used: 22200 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_027180538.1 G496_RS0118210 (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.20682.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-59 184.6 0.1 5.7e-59 184.5 0.1 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027180538.1 G496_RS0118210 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027180538.1 G496_RS0118210 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 184.5 0.1 5.7e-59 5.7e-59 1 157 [] 5 161 .. 5 161 .. 0.99 Alignments for each domain: == domain 1 score: 184.5 bits; conditional E-value: 5.7e-59 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 G v+k G ++dtdaiiP+r+l ttd++el++ +meg++ + k+v++ d++va +nfG+Gssre+a+++ lcl|NCBI__GCF_000429985.1:WP_027180538.1 5 GNVHKVGAHIDTDAIIPARFLVTTDPEELGANCMEGLEHGWIKRVKKNDIMVADENFGCGSSREHAPIS 73 89******************************************************************* PP TIGR02087 70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138 + aG+ v+a+sfarifyrn n+Gl+l+++ d + +i dGde+evd +kgei++++ e++++++++ lcl|NCBI__GCF_000429985.1:WP_027180538.1 74 ILGAGIPVVVAHSFARIFYRNGFNMGLILLEVGDNVSKISDGDELEVDADKGEIKNITTGETITCNPVP 142 *********************************99********************************** PP TIGR02087 139 dllleileeGGlleylkkr 157 +++eil++GGl+ey+kkr lcl|NCBI__GCF_000429985.1:WP_027180538.1 143 PFMKEILNSGGLVEYVKKR 161 *****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (166 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: 4.77 // [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