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 3610012 Dshi_3393 3-isopropylmalate dehydrogenase (RefSeq)
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__Dino:3610012 Length = 357 Score = 233 bits (594), Expect = 5e-66 Identities = 148/354 (41%), Positives = 209/354 (59%), Gaps = 29/354 (8%) Query: 4 ICVIEGDGIGKEVVPATIQVLE-----ATGLPFEFVYAEAGDEVYKRTGKALPEETIETA 58 I V +GDGIG E++ T+ +L A F G Y +TG+ALP +++ A Sbjct: 6 ITVFDGDGIGPEIMAPTLGLLRKLAGTAATYDLNFDSHPMGAGHYAQTGQALPRASLDAA 65 Query: 59 LDCDAVLFGAAG--------ETAADVIVKLRHILDTYANIRPVKAYKGVKC---LRPDID 107 DA+L A G T + +R LD YA +RPV+ G +D Sbjct: 66 RASDAILLSAMGLPDIRYPDGTEITPQIDIRIALDLYAGVRPVRIVPGHPTPLHAPGPVD 125 Query: 108 YVIVRENTEGLY--KGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGK-EGK 164 +V++RE+TEGL+ KG + + + T IT E++FRFAF LA +RK G+ EG+ Sbjct: 126 FVLIRESTEGLFHTKG-KGTVTKDHATETLQITRDTSEKLFRFAFALAAQRKASGRGEGR 184 Query: 165 VTCAHKANVLKLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNL 224 VTC KANV + F++IF A + D+ A+ Y+DAM ++++T+PQ FDV+VT N+ Sbjct: 185 VTCVDKANVFRAF-AFFREIFDAEAARHPDLIADHAYVDAMALWMVTRPQTFDVMVTENM 243 Query: 225 FGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLML 284 FGDILSD AG +GGLGLAPSA+IGD++ +F+P HG+APDIAG+ IANP A ILSA +ML Sbjct: 244 FGDILSDLGAGLMGGLGLAPSADIGDDNAVFQPCHGTAPDIAGRGIANPLAMILSAAMML 303 Query: 285 RYLG----EYEAA---DKVEKALEEVLALG-LTTPDLGGNLNTFEMAEEVAKRV 330 +L E A ++ +A+E VL G + T DLGGN +T E A VA ++ Sbjct: 304 DWLALRGQNAELATDGQRLREAVEAVLTEGRVLTRDLGGNASTEEAAAAVAAKL 357 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: 288 Number of extensions: 14 Number of successful extensions: 8 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: 357 Length adjustment: 29 Effective length of query: 304 Effective length of database: 328 Effective search space: 99712 Effective search space used: 99712 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