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_090220500.1 CV091_RS17260 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_002796795.1:WP_090220500.1 Length = 362 Score = 219 bits (559), Expect = 6e-62 Identities = 140/356 (39%), Positives = 200/356 (56%), Gaps = 31/356 (8%) Query: 4 ICVIEGDGIGKEVVPATIQVLEATGLPFE-----FVYAEAGDEVYKRTGKALPEETIETA 58 I V +GDGIG E+ T+ +L+ + F+ A AG Y+ TG + P+ ++ A Sbjct: 7 IAVFQGDGIGPEITAPTVSILKTLAAASDDYGLNFIDAPAGAAHYRDTGTSFPDASMAIA 66 Query: 59 LDCDAVLFGAAG--------ETAADVIVKLRHILDTYANIRPVKAYKGVKC-----LRPD 105 + DA+L A G T + LR L +A +RPV G + Sbjct: 67 TNADAILLSAMGLPDVRYPDGTEISPQIDLRKRLGLFAGVRPVTVRTGQTTPLNLPANKE 126 Query: 106 IDYVIVRENTEGLY--KGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGK-E 162 ID+V++RE+TEGL+ +G E+ T +IT + E++FRFAF LA RK G+ Sbjct: 127 IDFVLIRESTEGLFHTQGC-GEVSADEARETLLITREVSEKLFRFAFQLAHGRKAAGRGS 185 Query: 163 GKVTCAHKANVLKLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTS 222 G+VTC KANV + F+++F A+ + D+ A+ Y+DA ++++ KP FDV+VT Sbjct: 186 GRVTCVDKANVFRAF-AFFREMFDAEAKNHPDLTADHAYVDATALWMVQKPWEFDVLVTE 244 Query: 223 NLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVL 282 N+FGDILSD AG +GGLGLAPSA+IG + +F+P HGSAPDIAG+ +ANP A ILSA + Sbjct: 245 NMFGDILSDLGAGLMGGLGLAPSADIGLNNAVFQPCHGSAPDIAGQGVANPFAMILSAAM 304 Query: 283 MLRYLGEYEA-------ADKVEKALEEVLALGLT-TPDLGGNLNTFEMAEEVAKRV 330 ML +LG A ++ A+E V+A T T DLGG T A+ V V Sbjct: 305 MLEWLGTSHKIAALSRDAARLRTAVEHVVADESTLTRDLGGTAGTEAAAKAVLNAV 360 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: 300 Number of extensions: 15 Number of successful extensions: 5 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: 362 Length adjustment: 29 Effective length of query: 304 Effective length of database: 333 Effective search space: 101232 Effective search space used: 101232 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 26 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