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_157196862.1 MAEO_RS07600 homoisocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000017185.1:WP_157196862.1 Length = 344 Score = 326 bits (835), Expect = 6e-94 Identities = 174/343 (50%), Positives = 238/343 (69%), Gaps = 19/343 (5%) Query: 3 KICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALDCD 62 KICVIEGDGIGKEV+P T+++L+ G FEF+Y AG E +KR G A+PE+T++TA +CD Sbjct: 6 KICVIEGDGIGKEVIPETVRILKEIG-DFEFIYEHAGYECFKRCGDAIPEKTLKTAKECD 64 Query: 63 AVLFGAAGETAADV---------IVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRE 113 A+LFGA D I+ LR LD YAN+RP+ +ID++I+RE Sbjct: 65 AILFGAVSTPKLDETERKPYKSPILTLRKELDLYANVRPIHKLDNSDSSN-NIDFIIIRE 123 Query: 114 NTEGLYKGIEAEIDEG-ITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKAN 172 NTEGLY G+E +E + I+ R I++K +RI +FAF A + + KV+C HK+N Sbjct: 124 NTEGLYSGVEYYDEEKELAISERHISKKGSKRIIKFAFEYAVKHHRK----KVSCIHKSN 179 Query: 173 VLKLTDGLFKKIFYKVAEEYDD---IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDIL 229 +L++TDGLF IF + E+Y + I+ DY +DA MYI+ PQ+FDV+VT+NLFGDIL Sbjct: 180 ILRITDGLFLNIFNEFKEKYKNEYNIEGNDYLVDATAMYILKSPQMFDVIVTTNLFGDIL 239 Query: 230 SDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGE 289 SD A+G +GGLGLAPSANIGD +GLFEPVHGSAPDIAGK +ANP A +LSA +ML YL Sbjct: 240 SDEASGLLGGLGLAPSANIGDNYGLFEPVHGSAPDIAGKGVANPIAAVLSASMMLYYLDM 299 Query: 290 YEAADKVEKALEEVLALGLTTPDLGGNLNTFEMAEEVAKRVRE 332 E + ++ A+++VLA TPDLGGNL T E+++++ + +R+ Sbjct: 300 KEKSRLLKDAVKQVLAHKDITPDLGGNLKTKEVSDKIIEELRK 342 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: 372 Number of extensions: 16 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: 344 Length adjustment: 28 Effective length of query: 305 Effective length of database: 316 Effective search space: 96380 Effective search space used: 96380 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 Jul 25 2024. The underlying query database was built on Jul 25 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