Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate Synpcc7942_2548 Synpcc7942_2548 isopropylmalate isomerase small subunit
Query= curated2:Q8YX03 (202 letters) >FitnessBrowser__SynE:Synpcc7942_2548 Length = 202 Score = 268 bits (686), Expect = 4e-77 Identities = 126/202 (62%), Positives = 158/202 (78%) Query: 1 MVSEVREVTGRAIPLVGNDIDTDRIIPARYLKAITFDGLREGAFIDDRTALKGAHPFDQP 60 M SE+ EVTGRA+PLVGNDIDTDRIIPAR+L+++TFDGL FIDDR L+G HPFDQ Sbjct: 1 MGSEILEVTGRAVPLVGNDIDTDRIIPARFLRSVTFDGLGANVFIDDRQQLQGQHPFDQA 60 Query: 61 QYQDANILIVNRNFGCGSSREHAPQALSKWGIQAVIGESFAEIFFGNCVAIGVPCVTADE 120 QYQ A +L+VNRNFGCGSSREHAPQA++KWGIQA++GESFAEIFFGNC+++G+PCVTA Sbjct: 61 QYQGATVLVVNRNFGCGSSREHAPQAIAKWGIQAIVGESFAEIFFGNCLSLGIPCVTAGA 120 Query: 121 AIVKQLQELVAANPQANVSINLETLQVQVGDFIAPISIGEGTRSTFITGAWDACGQLVAN 180 A V +LQ +A++P V+++LE LQV+ G + A +++ G +G WDA GQLVAN Sbjct: 121 AAVAELQAAIASDPSQPVTVDLEELQVRRGAWSAELTLAPGPLQMLRSGQWDATGQLVAN 180 Query: 181 TEQVRVTAAKLPYVSWGKLAAS 202 E + TAA LPYV W +AAS Sbjct: 181 AEAIAQTAANLPYVGWQAIAAS 202 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: 178 Number of extensions: 2 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 Synpcc7942_2548 Synpcc7942_2548 (isopropylmalate isomerase 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.6419.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-38 118.0 0.0 2.6e-38 117.8 0.0 1.1 1 lcl|FitnessBrowser__SynE:Synpcc7942_2548 Synpcc7942_2548 isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2548 Synpcc7942_2548 isopropylmalate isomerase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 117.8 0.0 2.6e-38 2.6e-38 3 155 .. 4 151 .. 1 180 [. 0.92 Alignments for each domain: == domain 1 score: 117.8 bits; conditional E-value: 2.6e-38 TIGR00171 3 efkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgas 71 e+++ tG +vpl ++dtd iip +fl+ ++ G+g+++f + r + +G++p +++ qyqga+ lcl|FitnessBrowser__SynE:Synpcc7942_2548 4 EILEVTGRAVPLVGNDIDTDRIIPARFLRSVTFDGLGANVFIDDRQ-QLQGQHP-----FDQAQYQGAT 66 57889**************************************998.7778544.....6899****** PP TIGR00171 72 illarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkg 139 +l+++ nfGcGssrehap a++ +G++ i+ sfa+if++n++ g+ + + v el a ++ +++ lcl|FitnessBrowser__SynE:Synpcc7942_2548 67 VLVVNRNFGCGSSREHAPQAIAKWGIQAIVGESFAEIFFGNCLSLGIPCVTAGAAAVAELQAAIAsDPS 135 **************************************************************9998999 PP TIGR00171 140 lkltvdleaqkvkdse 155 + +tvdle+ +v+ + lcl|FitnessBrowser__SynE:Synpcc7942_2548 136 QPVTVDLEELQVRRGA 151 99*********99876 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.93 // [ok]
This GapMind analysis is from Apr 09 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