Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_049756062.1 PERMA_RS02530 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_000021565.1:WP_049756062.1 Length = 181 Score = 206 bits (524), Expect = 2e-58 Identities = 96/161 (59%), Positives = 126/161 (78%) Query: 4 IIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGGKNF 63 +I+G+VWKFG++++TD I+PARYL+ T P+ELA+ VM ADP+FP KVKPGDIIV GKNF Sbjct: 18 VIEGKVWKFGDDINTDEIIPARYLITTDPKELAKHVMEDADPEFPNKVKPGDIIVAGKNF 77 Query: 64 GCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDELEVN 123 GCGSSREHAPL LKGA I +IAESFARIFYRNAIN+GLP+IE + EGD ++++ Sbjct: 78 GCGSSREHAPLALKGAEIGAIIAESFARIFYRNAINLGLPIIESPEAARDAEEGDIIQID 137 Query: 124 LETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKKKM 164 ++ G I+N+T G+ + LPE + ++ EAGGLM Y K K+ Sbjct: 138 MDKGIIRNVTKGKEYTFKPLPESLRKVFEAGGLMEYAKDKL 178 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: 144 Number of extensions: 4 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: 181 Length adjustment: 19 Effective length of query: 149 Effective length of database: 162 Effective search space: 24138 Effective search space used: 24138 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: 44 (21.6 bits)
Align candidate WP_049756062.1 PERMA_RS02530 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR02084 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))
# 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/TIGR02084.hmm # target sequence database: /tmp/gapView.7763.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02084 [M=156] Accession: TIGR02084 Description: leud: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-79 248.9 0.0 9.2e-79 248.7 0.0 1.0 1 lcl|NCBI__GCF_000021565.1:WP_049756062.1 PERMA_RS02530 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021565.1:WP_049756062.1 PERMA_RS02530 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.7 0.0 9.2e-79 9.2e-79 1 155 [. 21 175 .. 21 176 .. 0.99 Alignments for each domain: == domain 1 score: 248.7 bits; conditional E-value: 9.2e-79 TIGR02084 1 gkvlkygdnvdtdviiparylntsdpkelakhcmedldkefkkkvkegdilvagknfgcgssrehapia 69 gkv+k+gd+++td+iiparyl t+dpkelakh+med+d ef +kvk gdi+vagknfgcgssrehap+a lcl|NCBI__GCF_000021565.1:WP_049756062.1 21 GKVWKFGDDINTDEIIPARYLITTDPKELAKHVMEDADPEFPNKVKPGDIIVAGKNFGCGSSREHAPLA 89 89******************************************************************* PP TIGR02084 70 ikasgiscviaksfarifyrnainiglpiveseeavdeleegdevevdlekgiiknvkkgkeykakpfp 138 +k + i ++ia sfarifyrnain+glpi+es ea+ ++eegd++++d++kgii+nv+kgkey kp p lcl|NCBI__GCF_000021565.1:WP_049756062.1 90 LKGAEIGAIIAESFARIFYRNAINLGLPIIESPEAARDAEEGDIIQIDMDKGIIRNVTKGKEYTFKPLP 158 ********************************************************************* PP TIGR02084 139 eflkeilkaegllnyvk 155 e l+++++a+gl++y+k lcl|NCBI__GCF_000021565.1:WP_049756062.1 159 ESLRKVFEAGGLMEYAK 175 ***************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (156 nodes) Target sequences: 1 (181 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.80 // [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