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_014449910.1 LFE_RS08995 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000284315.1:WP_014449910.1 Length = 416 Score = 147 bits (371), Expect = 5e-40 Identities = 117/354 (33%), Positives = 167/354 (47%), Gaps = 67/354 (18%) Query: 7 IEGDGIGKEVVPATIQVLEATGLP----------FEFVYAEAGDEVYKRTGKALPEETI- 55 I GDG G+++ A+++V +A FE E +EVY LPE+T+ Sbjct: 34 IAGDGTGQDIWNASVRVFDAAVKKAFGGKKKVEWFEVYAGEKANEVYG-PNTWLPEDTLA 92 Query: 56 ---ETALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKCLR-PD-IDYVI 110 E + L G + V LR LD YA +RPV + ++ P+ +D VI Sbjct: 93 ANREFKMSIKGPLTTPVGGGIRSINVALRQELDLYACVRPVSWFGSPSPVKHPELVDMVI 152 Query: 111 VRENTEGLYKGIEAEIDEGI-----------------------TIATRVITEKACERIFR 147 RENTE +Y GIE + + +I + ++E+ +R+ R Sbjct: 153 FRENTEDIYAGIEWATGDPVIQELYKVFEKAGVMKKIRFPKTASIGIKPVSEEGTKRLVR 212 Query: 148 FA--FNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEE--------YDD--- 194 A F LA RK VT HK N++K T+G F+K Y+VA++ +DD Sbjct: 213 AAIRFALANNRKS------VTLVHKGNIMKFTEGYFRKWGYEVAKDEFGDKTVSWDDCGG 266 Query: 195 ------IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANI 248 + +D DA I+ + +DV+ T NL GD LSD A VGG+G+AP ANI Sbjct: 267 NAPAGKLLIKDEIADAFLQKILLRANEYDVIATLNLNGDYLSDALAAQVGGIGIAPGANI 326 Query: 249 GDEHG--LFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKAL 300 E G +FE HG+AP A + NP A ILS +M RY+G E AD + K L Sbjct: 327 NYETGAAVFEATHGTAPKYANQDKVNPGAVILSGEMMFRYMGWNEVADLILKGL 380 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: 326 Number of extensions: 26 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: 416 Length adjustment: 30 Effective length of query: 303 Effective length of database: 386 Effective search space: 116958 Effective search space used: 116958 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