Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_011320658.1 AVA_RS20105 3-isopropylmalate dehydratase small subunit
Query= curated2:Q8YX03 (202 letters) >NCBI__GCF_000204075.1:WP_011320658.1 Length = 202 Score = 390 bits (1002), Expect = e-114 Identities = 194/201 (96%), Positives = 197/201 (98%) Query: 1 MVSEVREVTGRAIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKGAHPFDQP 60 MVSEV+EVTGR IPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKG HPFDQP Sbjct: 1 MVSEVKEVTGRGIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKGEHPFDQP 60 Query: 61 QYQDANILIVNRNFGCGSSREHAPQALSKWGIQAVIGESFAEIFFGNCVAIGVPCVTADE 120 QYQ ANILIVNRNFGCGSSREHAPQALSKWGIQ+VIGESFAEIFFGNCVAIGVPCVTADE Sbjct: 61 QYQGANILIVNRNFGCGSSREHAPQALSKWGIQSVIGESFAEIFFGNCVAIGVPCVTADE 120 Query: 121 AIVKQLQELVAANPQANVSINLETLQVQVGDFIAPISIGEGTRSTFITGAWDACGQLVAN 180 AIVKQLQELVAANPQANVSINLETLQVQVGDF APISIGEGTRSTFITGAWDACGQLVAN Sbjct: 121 AIVKQLQELVAANPQANVSINLETLQVQVGDFTAPISIGEGTRSTFITGAWDACGQLVAN 180 Query: 181 TEQVRVTAAKLPYVSWGKLAA 201 TEQVRVT+AKLPYVSWGKLAA Sbjct: 181 TEQVRVTSAKLPYVSWGKLAA 201 Lambda K H 0.320 0.136 0.403 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: 254 Number of extensions: 1 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: 202 Length of database: 202 Length adjustment: 21 Effective length of query: 181 Effective length of database: 181 Effective search space: 32761 Effective search space used: 32761 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 bits)
Align candidate WP_011320658.1 AVA_RS20105 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR00171 (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/TIGR00171.hmm # target sequence database: /tmp/gapView.1081205.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00171 [M=188] Accession: TIGR00171 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-40 124.5 0.0 2.7e-40 124.3 0.0 1.0 1 NCBI__GCF_000204075.1:WP_011320658.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011320658.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 124.3 0.0 2.7e-40 2.7e-40 3 175 .. 4 170 .. 2 184 .. 0.91 Alignments for each domain: == domain 1 score: 124.3 bits; conditional E-value: 2.7e-40 TIGR00171 3 efkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasilla 75 e+k+ tG +pl ++dtd iip ++lk+i+ G+++ +f + r kG e +++pqyqga+il++ NCBI__GCF_000204075.1:WP_011320658.1 4 EVKEVTGRGIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRT-ALKG-----EHPFDQPQYQGANILIV 70 67899**************************************998.6677.....56679************ PP TIGR00171 76 renfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdle 147 + nfGcGssrehap al+ +G++++i sfa+if++n++ g+ + +e++v++l +lv+ n+ +++++le NCBI__GCF_000204075.1:WP_011320658.1 71 NRNFGCGSSREHAPQALSKWGIQSVIGESFAEIFFGNCVAIGVPCVTADEAIVKQLQELVAaNPQANVSINLE 143 ***********************************************************999*********** PP TIGR00171 148 aqkvkdsegkvysfeidefrkhcllnGl 175 + +v++++ + i e + ++ G NCBI__GCF_000204075.1:WP_011320658.1 144 TLQVQVGD-FTAPISIGEGTRSTFITGA 170 ********.7888888888888777774 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (202 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.83 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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