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 209413 DVU0477 isocitrate dehydrogenase, NADP-dependent
Query= SwissProt::Q58130 (333 letters) >MicrobesOnline__882:209413 Length = 380 Score = 191 bits (485), Expect = 3e-53 Identities = 126/368 (34%), Positives = 187/368 (50%), Gaps = 51/368 (13%) Query: 7 IEGDGIGKEVVPATIQVLEAT-------GLPFEFVYAEAGDEVYKRTGKALPEETIETAL 59 IEGDGIG EV A V++A E+ AG++ ++ TG+ LP+ T++T Sbjct: 8 IEGDGIGPEVWKAARPVIDAAVEKSYGDSRSIEWKELLAGEKAHRETGEYLPQSTLDTLA 67 Query: 60 DCDAVLFGAAGETAA----DVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVIVR 112 + + G G + V +R LD YA IRP++ + G+ RPD +D V+ R Sbjct: 68 TAELAIKGPLGTPVGKGFRSLNVTMRQTLDLYACIRPIRYFDGIMSPVKRPDLVDMVVFR 127 Query: 113 ENTEGLYKGIE--------------------AEIDEGITIATRVITEKACERIFRFAFNL 152 ENTE +Y GIE A++D + + +TEK +R+ R A Sbjct: 128 ENTEDVYAGIEYRAGTPEAKRLIAFLRDELGAKVDIEAAVGIKPMTEKGSKRLVRRALRF 187 Query: 153 ARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVA-EEYDDIKA------------ED 199 A ++K+ +T HK N++K T+G F++ Y+VA +E+ D+ +D Sbjct: 188 AIDQKRPN----LTLVHKGNIMKFTEGGFREWGYEVARDEFADLTTTETEGTAGRLVVKD 243 Query: 200 YYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVH 259 DAM ++ +PQ + V+ TSNL GD +SD A VGGLGLAP N+ D FE H Sbjct: 244 RIADAMFQEVLIRPQQYSVIATSNLNGDYISDALAAQVGGLGLAPGVNMSDSLAFFEATH 303 Query: 260 GSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTTPDLGGNLNT 319 G+AP IAG+ ANP + IL LML ++G EAA+++ KA+ E +A T DL + Sbjct: 304 GTAPTIAGQDKANPGSLILCGALMLEHMGWNEAAERIYKAVNEAIASRRVTVDLATQMEN 363 Query: 320 FEMAEEVA 327 VA Sbjct: 364 ATTVGTVA 371 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: 272 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: 380 Length adjustment: 29 Effective length of query: 304 Effective length of database: 351 Effective search space: 106704 Effective search space used: 106704 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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