Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_092348734.1 BLU87_RS11905 3-isopropylmalate dehydratase small subunit
Query= curated2:A1K4A2 (212 letters) >NCBI__GCF_900107645.1:WP_092348734.1 Length = 216 Score = 302 bits (773), Expect = 4e-87 Identities = 142/211 (67%), Positives = 167/211 (79%) Query: 1 MKPFTVLDAIVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDVGQPGQDCSN 60 M+ FT L +VAPLDR+N+DTDAIIPKQFLKSIKR+GFGP LFDEWRYLD G+P DCS+ Sbjct: 1 MEKFTQLTGLVAPLDRSNIDTDAIIPKQFLKSIKRTGFGPYLFDEWRYLDHGEPDMDCSD 60 Query: 61 RPKNPDFVLNQARYQGAQVLLARDNFGCGSSREHAPWALEDYGFRVIIAPSFADIFFNNS 120 RP NPDF+LN RYQGAQ+LLARDNFGCGSSREHAPWAL DYGFRVIIAPSFADIF+NN Sbjct: 61 RPLNPDFILNHPRYQGAQILLARDNFGCGSSREHAPWALLDYGFRVIIAPSFADIFYNNC 120 Query: 121 FKNGLLPIKLDAAELDVLFQQCEATEGYRLKVDLAAQTITRPDGKAIAFDVDPFRKECLL 180 FKNG+LPI LD +D LF GY+++V+L ++T P+GK +F+VDPFR+ CLL Sbjct: 121 FKNGILPIVLDTDNIDELFTAVMDQPGYKIEVNLETTSLTSPNGKMYSFEVDPFRRHCLL 180 Query: 181 NGWDDIGLTLRHADKIRDFEAKRRAEHPYYF 211 NG DDIGLTL DKI +E R +P+ F Sbjct: 181 NGLDDIGLTLEKVDKITAYEDSHRLANPWLF 211 Lambda K H 0.323 0.141 0.441 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: 211 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: 212 Length of database: 216 Length adjustment: 22 Effective length of query: 190 Effective length of database: 194 Effective search space: 36860 Effective search space used: 36860 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 45 (21.9 bits)
Align candidate WP_092348734.1 BLU87_RS11905 (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.21942.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-90 288.4 0.0 1.5e-90 288.2 0.0 1.1 1 lcl|NCBI__GCF_900107645.1:WP_092348734.1 BLU87_RS11905 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092348734.1 BLU87_RS11905 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 288.2 0.0 1.5e-90 1.5e-90 1 188 [] 1 196 [. 1 196 [. 0.94 Alignments for each domain: == domain 1 score: 288.2 bits; conditional E-value: 1.5e-90 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkep.......npefvl 62 m++f +ltGlv+pld+ n+dtdaiipkqflk ikrtGfg +lf ewryld+ + np+f+l lcl|NCBI__GCF_900107645.1:WP_092348734.1 1 MEKFTQLTGLVAPLDRSNIDTDAIIPKQFLKSIKRTGFGPYLFDEWRYLDHGEPDMdcsdrplNPDFIL 69 899*********************************************9864322111222349***** PP TIGR00171 63 nvpqyqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveel 131 n+p+yqga+illar+nfGcGssrehapwal dyGf+viiapsfadifynn+fkng+lpi l++++++el lcl|NCBI__GCF_900107645.1:WP_092348734.1 70 NHPRYQGAQILLARDNFGCGSSREHAPWALLDYGFRVIIAPSFADIFYNNCFKNGILPIVLDTDNIDEL 138 ********************************************************************* PP TIGR00171 132 lalvk.nkglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 ++ v +g k++v+le+ +++ +gk+ysfe+d+fr+hcllnGld+igltl k d+i lcl|NCBI__GCF_900107645.1:WP_092348734.1 139 FTAVMdQPGYKIEVNLETTSLTSPNGKMYSFEVDPFRRHCLLNGLDDIGLTLEKVDKI 196 **999788**********************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (216 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.16 // [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