Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_019895996.1 A377_RS0108990 3-isopropylmalate dehydratase small subunit
Query= uniprot:Q845W4 (216 letters) >NCBI__GCF_000384235.1:WP_019895996.1 Length = 219 Score = 294 bits (753), Expect = 8e-85 Identities = 138/210 (65%), Positives = 164/210 (78%) Query: 1 MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60 ++KFT +VAP+DR NVDTDAIIPKQFLKSIKRTGFGPN FDEWRY D G+PG DNS+ Sbjct: 3 LQKFTKFDALVAPMDRANVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYEDVGQPGVDNSQ 62 Query: 61 RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120 RPL DFVLNQPRYQGA +L+ R+NFGCGSSREHAPWAL+ YGF I+APSFADIFFNN Sbjct: 63 RPLKKDFVLNQPRYQGARLLLARENFGCGSSREHAPWALKDYGFDVIVAPSFADIFFNNS 122 Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180 FKNG+LPIVL + V+ L A GY LT+DLE Q + PDG F++ +FRK+CLL Sbjct: 123 FKNGILPIVLPAETVEQLFQAVYAQEGYSLTVDLENQQLVQPDGTTIAFDVDSFRKHCLL 182 Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210 NG DDI LTL+ +D+I+ FEA+ + PWL Sbjct: 183 NGLDDIALTLQQSDEIKAFEADYRQRAPWL 212 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: 222 Number of extensions: 7 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: 216 Length of database: 219 Length adjustment: 22 Effective length of query: 194 Effective length of database: 197 Effective search space: 38218 Effective search space used: 38218 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 WP_019895996.1 A377_RS0108990 (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.2659.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-88 279.3 0.0 1.1e-87 278.8 0.0 1.2 1 lcl|NCBI__GCF_000384235.1:WP_019895996.1 A377_RS0108990 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895996.1 A377_RS0108990 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.8 0.0 1.1e-87 1.1e-87 2 188 .] 4 198 .. 3 198 .. 0.93 Alignments for each domain: == domain 1 score: 278.8 bits; conditional E-value: 1.1e-87 TIGR00171 2 kefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewrylde..kGkep.....npefvln 63 ++f k++ lv+p+d+anvdtdaiipkqflk ikrtGfg +lf ewry d+ G ++ + +fvln lcl|NCBI__GCF_000384235.1:WP_019895996.1 4 QKFTKFDALVAPMDRANVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYEDVgqPGVDNsqrplKKDFVLN 72 67999******************************************98522233321112367***** PP TIGR00171 64 vpqyqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveell 132 +p+yqga +llarenfGcGssrehapwalkdyGf vi+apsfadif+nnsfkng+lpi l+ e+ve+l+ lcl|NCBI__GCF_000384235.1:WP_019895996.1 73 QPRYQGARLLLARENFGCGSSREHAPWALKDYGFDVIVAPSFADIFFNNSFKNGILPIVLPAETVEQLF 141 ********************************************************************* PP TIGR00171 133 alvk.nkglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 + v +g ltvdle+q++ + +g ++ f++d+frkhcllnGld+i+ltlq+ dei lcl|NCBI__GCF_000384235.1:WP_019895996.1 142 QAVYaQEGYSLTVDLENQQLVQPDGTTIAFDVDSFRKHCLLNGLDDIALTLQQSDEI 198 *988799***********************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (219 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: 6.60 // [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