Align 2-(omega-methylthio)alkylmalate dehydratase (subunit 1/2) (EC 4.2.1.170); 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_012465697.1 CLIM_RS03695 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q9LYT7 (253 letters) >NCBI__GCF_000020465.1:WP_012465697.1 Length = 188 Score = 154 bits (388), Expect = 2e-42 Identities = 85/182 (46%), Positives = 112/182 (61%), Gaps = 9/182 (4%) Query: 75 GLCFVLKDNIDTDQIIPAEYGTLIPSIPEDREKLGSFALNGLPKFYNER------FVVPG 128 G +VL NIDTDQIIPAE+ S PE+ + G +AL+G+P FV G Sbjct: 7 GKAYVLGKNIDTDQIIPAEHLVYSLSDPEEVKLYGKYALSGVPPEQGGLPQGDIPFVTEG 66 Query: 129 EMKSKYSVIIGGDNFGCGSSREHAPVCLGAAGAKAVVAESYARIFFRNCVATGEIFPLES 188 S Y++I+ G NFGCGSSREHAP L AGAKA+VAESYARIF+RNCV G + P E+ Sbjct: 67 SFHSDYTIIVAGPNFGCGSSREHAPFALQVAGAKAIVAESYARIFYRNCVDGGFVIPYET 126 Query: 189 EVRICDECKTGDVVTIEHKEDGSSLLINHTTRKEYKLKPLGDAGPVIDAGGIFAYARKAG 248 V + KTGD + I+ + ++ + N T + L PLGD ++ AGGIFAYAR+ Sbjct: 127 SVPLTGVIKTGDELKIDIE---ANTVTNLETNITFTLNPLGDVFSIVRAGGIFAYARQEN 183 Query: 249 MI 250 ++ Sbjct: 184 LM 185 Lambda K H 0.317 0.134 0.391 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: 165 Number of extensions: 8 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: 253 Length of database: 188 Length adjustment: 22 Effective length of query: 231 Effective length of database: 166 Effective search space: 38346 Effective search space used: 38346 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 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_012465697.1 CLIM_RS03695 (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.29875.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-38 118.1 0.0 1.1e-37 115.3 0.0 1.9 1 lcl|NCBI__GCF_000020465.1:WP_012465697.1 CLIM_RS03695 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020465.1:WP_012465697.1 CLIM_RS03695 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.3 0.0 1.1e-37 1.1e-37 1 156 [. 7 181 .. 7 182 .. 0.81 Alignments for each domain: == domain 1 score: 115.3 bits; conditional E-value: 1.1e-37 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrtt..d...lkelakhamegidpe..........fakkvreG...... 48 G+++ +G ++dtd+iiP++ l + d +k ++k+a+ g+ pe f v eG lcl|NCBI__GCF_000020465.1:WP_012465697.1 7 GKAYVLGKNIDTDQIIPAEHLVYSlsDpeeVKLYGKYALSGVPPEqgglpqgdipF---VTEGsfhsdy 72 89****************99865322411255679*******99944433332222...5555333323 PP TIGR02087 49 dvivaGknfGiGssreqaalalkaaGvaaviaesfarifyrnainvGlplivae..dvtelikdGdeve 115 +ivaG nfG+Gssre+a++al+ aG +a++aes+arifyrn ++ G+++ + t +ik Gde++ lcl|NCBI__GCF_000020465.1:WP_012465697.1 73 TIIVAGPNFGCGSSREHAPFALQVAGAKAIVAESYARIFYRNCVDGGFVIPYETsvPLTGVIKTGDELK 141 69*********************************************7654444235699********* PP TIGR02087 116 vdlekgeirkvakkevlkleeledllleileeGGlleylkk 156 +d+e + + +++ + +++l++l d+ +i+++GG+ y ++ lcl|NCBI__GCF_000020465.1:WP_012465697.1 142 IDIEANTVTNLETNITFTLNPLGDV-FSIVRAGGIFAYARQ 181 ********************99996.69*********9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (188 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: 00:00:00.01 # Mc/sec: 2.08 // [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