Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate GFF1851 PS417_09415 3-isopropylmalate dehydratase
Query= uniprot:Q845W4 (216 letters) >FitnessBrowser__WCS417:GFF1851 Length = 204 Score = 193 bits (490), Expect = 2e-54 Identities = 101/211 (47%), Positives = 130/211 (61%), Gaps = 9/211 (4%) Query: 1 MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60 ++ FT+ TG AP+ N+DTD I+PKQFLK I R+G F + R+L GEP Sbjct: 3 LQPFTLVTGKAAPMLAANIDTDVIMPKQFLKGIDRSGLDRGLFFDLRFLSSGEP------ 56 Query: 61 RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120 NP+FVLNQP +QGAS +V NFGCGSSREHA W L+Q G RA+I SFA IF++NC Sbjct: 57 ---NPEFVLNQPAWQGASFMVVGPNFGCGSSREHAVWGLKQMGIRALIGSSFAGIFYDNC 113 Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180 +NG+L I L E + L + Q+++DLEAQ +R DG F+I RK LL Sbjct: 114 QRNGVLLITLDEAVLQTLGKTVSQADQAQISVDLEAQQIRLADGEVIAFQIDTLRKSALL 173 Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWLN 211 G D IG TL+ +D+I+ FE L PWLN Sbjct: 174 LGLDAIGSTLQRSDEIKAFERRHLQANPWLN 204 Lambda K H 0.322 0.141 0.437 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: 140 Number of extensions: 8 Number of successful extensions: 2 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: 216 Length of database: 204 Length adjustment: 21 Effective length of query: 195 Effective length of database: 183 Effective search space: 35685 Effective search space used: 35685 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate GFF1851 PS417_09415 (3-isopropylmalate dehydratase)
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.14852.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-66 210.0 0.0 1.6e-66 209.8 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF1851 PS417_09415 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1851 PS417_09415 3-isopropylmalate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.8 0.0 1.6e-66 1.6e-66 2 188 .] 4 189 .. 3 189 .. 0.97 Alignments for each domain: == domain 1 score: 209.8 bits; conditional E-value: 1.6e-66 TIGR00171 2 kefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillar 76 ++f tG+++p+ +an+dtd i+pkqflk i+r G+++ lf++ r+l + G epnpefvln+p +qgas ++++ lcl|FitnessBrowser__WCS417:GFF1851 4 QPFTLVTGKAAPMLAANIDTDVIMPKQFLKGIDRSGLDRGLFFDLRFL-SSG-EPNPEFVLNQPAWQGASFMVVG 76 689999*****************************************6.567.9********************* PP TIGR00171 77 enfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqk 150 nfGcGssreha w lk+ G++ +i sfa ify+n+ +ng+l i l+e+ ++ l ++v+ + +++vdleaq+ lcl|FitnessBrowser__WCS417:GFF1851 77 PNFGCGSSREHAVWGLKQMGIRALIGSSFAGIFYDNCQRNGVLLITLDEAVLQTLGKTVSqADQAQISVDLEAQQ 151 ****************************************************9999999878899********** PP TIGR00171 151 vkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 ++ ++g+v+ f+id+ rk ll Gld ig tlq+ dei lcl|FitnessBrowser__WCS417:GFF1851 152 IRLADGEVIAFQIDTLRKSALLLGLDAIGSTLQRSDEI 189 ***********************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (204 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: 6.59 // [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