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_012566126.1 RC1_RS04300 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000016185.1:WP_012566126.1 Length = 483 Score = 222 bits (565), Expect = 2e-62 Identities = 127/317 (40%), Positives = 188/317 (59%), Gaps = 10/317 (3%) Query: 3 KICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKR-----TGKALPEETIET 57 K+ + GDGIG E++ AT+++LEA G E+ + G+ VY+R A + T Sbjct: 6 KVTIARGDGIGPEIMDATLEILEAAGAALEYEEIQIGESVYRRGILNGMEPAAWDSLRRT 65 Query: 58 ALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKG-VKCLRPDIDYVIVRENTE 116 + A + G + V +R L YANIRP +Y V P +D VIVREN E Sbjct: 66 RVFLKAPITTPQGGGYKSLNVTIRGALGLYANIRPCVSYHPFVNTKHPQMDVVIVRENEE 125 Query: 117 GLYKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKL 176 LY GIE + +T A ++I+ E+I R+AF AR + KVT K N++K+ Sbjct: 126 DLYAGIEYRQTQDVTQAVKLISRPGSEKIIRYAFEYARANHRR----KVTAFVKDNIMKI 181 Query: 177 TDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGT 236 +DGLF ++F ++A EY +I+ E ID + P+ FDV+VT NL+GDI+SD AA Sbjct: 182 SDGLFHRVFDEIAAEYPEIEHETMIIDIGAARLADTPEQFDVIVTLNLYGDIISDIAAQI 241 Query: 237 VGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKV 296 G +GLA S+NIGD+ +FE +HGSAP+IAGK IANP+ IL++V+ML ++G+ EAA+++ Sbjct: 242 TGSVGLAGSSNIGDQCAMFEAIHGSAPNIAGKGIANPSGLILASVMMLVHVGQAEAAERI 301 Query: 297 EKALEEVLALGLTTPDL 313 A ++ G+ T D+ Sbjct: 302 HNAWLRMIEDGIHTVDI 318 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: 373 Number of extensions: 24 Number of successful extensions: 4 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: 483 Length adjustment: 31 Effective length of query: 302 Effective length of database: 452 Effective search space: 136504 Effective search space used: 136504 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: 50 (23.9 bits)
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