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_028585044.1 G494_RS0113985 isocitrate dehydrogenase (NADP(+))
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000429965.1:WP_028585044.1 Length = 405 Score = 180 bits (457), Expect = 5e-50 Identities = 130/364 (35%), Positives = 182/364 (50%), Gaps = 63/364 (17%) Query: 7 IEGDGIGKEVVPATIQVLEA------TGLP-FEFVYAEAGDEVYKRTGKALPEETIET-- 57 IEGDGIG ++ A V++A TG ++ AG++ TG+ LP+ET++ Sbjct: 25 IEGDGIGPDIWAAARNVVDAAIKKTYTGQKKINWLEIFAGEKALDTTGEWLPQETLDALK 84 Query: 58 --ALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKCLRP-----DIDYVI 110 + L GE + V LR +LD YA +RPV+ Y+GV + P D+D VI Sbjct: 85 KYVVGIKGPLTTPVGEGMRSLNVTLRQVLDLYACVRPVRYYQGV--VSPVKEPGDVDMVI 142 Query: 111 VRENTEGLYKGIE--------------------AEIDEGITIATRVITEKACERIFRFAF 150 RENTE +Y GIE A+I + I + I+E +R+ R A Sbjct: 143 FRENTEDVYAGIEWQAGTDQANKVIEFLRNEMGADIRDNSGIGIKPISEFGTKRLVRKAI 202 Query: 151 NLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVA-EEYDDIKA------------ 197 A + ++ VT HK N++K T+G F+ Y++A EE+ DI Sbjct: 203 QYAIDHQR----DSVTLVHKGNIMKFTEGAFRNWGYELAAEEFADITISEDDLWKHHNGE 258 Query: 198 --------EDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIG 249 +D DAM I+ +P+ + V+ NL GD +SD A VGGLG+AP ANIG Sbjct: 259 LPPGKILIKDRIADAMFQQILLRPREYSVLAMPNLNGDYMSDALAAQVGGLGIAPGANIG 318 Query: 250 DEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLT 309 D LFE HG+AP AG NP + +LSAV+ML YLG EAAD ++ ALE + Sbjct: 319 DGVALFEATHGTAPKYAGLDKVNPGSVLLSAVMMLEYLGWQEAADAIKTALETTIGDKTV 378 Query: 310 TPDL 313 T DL Sbjct: 379 TYDL 382 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: 324 Number of extensions: 18 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: 405 Length adjustment: 30 Effective length of query: 303 Effective length of database: 375 Effective search space: 113625 Effective search space used: 113625 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 Apr 10 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