Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_012966595.1 FERP_RS10670 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000025505.1:WP_012966595.1 Length = 325 Score = 403 bits (1035), Expect = e-117 Identities = 210/328 (64%), Positives = 254/328 (77%), Gaps = 5/328 (1%) Query: 3 KICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALDCD 62 +I VI GDGIGKEV A + +LE LPFE+V+ EAGDE K+ GK LP+ET+E C Sbjct: 2 RIAVIPGDGIGKEVTEAAMLILENLDLPFEYVWLEAGDEAEKKYGKPLPDETLEEVKRCK 61 Query: 63 AVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEGLYKGI 122 AVLFGAAGETAADVIVKLR L+TYAN+RP K+++GVK + ++D VIVRENTE LYKGI Sbjct: 62 AVLFGAAGETAADVIVKLRQELETYANVRPAKSFEGVKSIHKNVDMVIVRENTECLYKGI 121 Query: 123 EAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFK 182 E E+D G+ A R+I+ KA ERI RFAF LA+ K+ +VT HKANV++ T GLFK Sbjct: 122 EFEVD-GVAEAVRIISRKASERIVRFAFELAKREKRK----RVTALHKANVMRKTCGLFK 176 Query: 183 KIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGL 242 ++FY+VA EY+ I+A DYYIDA MYI P FDV+VT+N+FGDI+SD AAG VGGLGL Sbjct: 177 RVFYEVAREYERIEANDYYIDAACMYIAMDPWRFDVIVTTNMFGDIVSDLAAGIVGGLGL 236 Query: 243 APSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEE 302 APSANIGDE+ +FEPVHG+A DIAGK IANPTA IL+A +MLR+LG E A KVEKA+E+ Sbjct: 237 APSANIGDEYAIFEPVHGAAFDIAGKGIANPTAMILTASMMLRHLGFEEEAKKVEKAVEK 296 Query: 303 VLALGLTTPDLGGNLNTFEMAEEVAKRV 330 VLA G TTPDLGGNL T EMAEE+ K + Sbjct: 297 VLAEGKTTPDLGGNLKTMEMAEEILKAI 324 Lambda K H 0.318 0.138 0.390 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: 359 Number of extensions: 12 Number of successful extensions: 3 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: 333 Length of database: 325 Length adjustment: 28 Effective length of query: 305 Effective length of database: 297 Effective search space: 90585 Effective search space used: 90585 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
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