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_011024146.1 MA_RS22270 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000007345.1:WP_011024146.1 Length = 342 Score = 226 bits (575), Expect = 8e-64 Identities = 135/337 (40%), Positives = 194/337 (57%), Gaps = 14/337 (4%) Query: 6 VIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTG--KALPEETIETALDCDA 63 VI+GDG+G E+V A ++V A G EFV EAG ++ G +P+ET + DA Sbjct: 7 VIKGDGVGPELVEAMLKVANAAGTDVEFVMCEAGAGWWEEHGGNSLVPDETWQILDSSDA 66 Query: 64 VLFGAAGETAA-----DVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEGL 118 G V V +R D YAN+RP+K + D++ V VRE TEGL Sbjct: 67 CFKGPTTTPGGIGSPRSVAVSIRRKYDLYANVRPIKTFPNSNAPLGDVEMVCVREGTEGL 126 Query: 119 YKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLTD 178 Y G E ++ + ++IA R IT A +I R+AF E K+ G + V HK+N+LKLT Sbjct: 127 YIGEEIQLTDDVSIAIRKITRTASGKIARYAFE---EAKRRGYD-TVVPIHKSNILKLTC 182 Query: 179 GLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFD--VVVTSNLFGDILSDGAAGT 236 G F + KVA++Y +I+ Y+ID + +I PQ+F+ V++++NLF D++S+ + Sbjct: 183 GSFLEEVEKVAQDYPNIEVWPYHIDNIAQQLIKNPQIFNKKVLLSTNLFMDVISEECSAL 242 Query: 237 VGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKV 296 VG +GL SAN+GD +FEP HGSAP AG NP AT+L+ ML YLGE E ++ + Sbjct: 243 VGSIGLIYSANLGDNFAMFEPAHGSAPKYAGLDKVNPVATVLAGAWMLDYLGEKEKSEAI 302 Query: 297 EKALEEVLALG-LTTPDLGGNLNTFEMAEEVAKRVRE 332 KA E V++ G T D+GGN +MA+E+AK E Sbjct: 303 FKATERVISEGKYVTYDVGGNAKLSQMADEIAKYTAE 339 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: 291 Number of extensions: 15 Number of successful extensions: 6 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: 342 Length adjustment: 28 Effective length of query: 305 Effective length of database: 314 Effective search space: 95770 Effective search space used: 95770 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