Align isocitrate dehydrogenase (NAD+) (EC 1.1.1.41) (characterized)
to candidate WP_010936227.1 DET_RS02445 isocitrate/isopropylmalate dehydrogenase family protein
Query= BRENDA::Q945K7 (374 letters) >NCBI__GCF_000011905.1:WP_010936227.1 Length = 359 Score = 306 bits (784), Expect = 6e-88 Identities = 160/331 (48%), Positives = 219/331 (66%), Gaps = 21/331 (6%) Query: 47 TLFPGDGIGPEIAESVKKVFTTAGVPIEWEEHYVGTEIDPRTQSFLTWESLESVRRNKVG 106 TL PGDGIGPEI+E+ ++V GV WE G ++ + L LES+R+NKV Sbjct: 6 TLIPGDGIGPEISEATRRVLEATGVKFNWEIVNAGADVVAEYGTPLPDMVLESIRKNKVA 65 Query: 107 LKGPMATPIGKGHRSLNLTLRKELNLYANVRPCYSLPGYKTRYDDVDLITIRENTEGEYS 166 +KGP+ TP+G G RS+N+ +RK LNLY +RPC + PG +RYD+VD++ +REN E Y+ Sbjct: 66 IKGPVTTPVGSGFRSVNVGMRKALNLYTCLRPCKTYPGVPSRYDNVDIVIVRENMEDLYA 125 Query: 167 GLEHQ--------VVRGVVESLKIITRQAS------------LRVAEYAFLYAKTHGRER 206 G+E + ++ + E+ K+ R S R+ +AF YA+ + R+R Sbjct: 126 GIEFEKGSPEALRLIEFIKENKKVEIRADSGISIKPISVFGTERIFRWAFKYARDNKRKR 185 Query: 207 VSAIHKANIMQKTDGLFLKCCREVAEKYPEITYEEVVIDNCCMMLVKNPALFDVLVMPNL 266 V+A+HKANIM+ +DGLFL R+VAE+YPEI +E+ ++DN M LVKNP+ FD+LV PNL Sbjct: 186 VTAVHKANIMKYSDGLFLAIGRKVAEEYPEIEFEDRIVDNMTMQLVKNPSQFDILVCPNL 245 Query: 267 YGDIISDLCAGLVGGLGLTPSCNIGEDGVALAEAVHGSAPDIAGKNLANPTALLLSGVMM 326 YGDI+SDLCAGLVGGLG+ P NIG D AL E HGSAP G N NP A++LSGV+M Sbjct: 246 YGDILSDLCAGLVGGLGVAPGANIG-DEYALFEPTHGSAPKYKGMNKVNPMAMMLSGVLM 304 Query: 327 LRHLKFNEQAEQIHSAIINTIAEGKYRTADL 357 LR+LK + A+++ +AI IAEGK T D+ Sbjct: 305 LRYLKEEKAADKLENAIAAVIAEGKSVTYDM 335 Lambda K H 0.318 0.134 0.389 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: 363 Number of extensions: 17 Number of successful extensions: 4 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: 374 Length of database: 359 Length adjustment: 30 Effective length of query: 344 Effective length of database: 329 Effective search space: 113176 Effective search space used: 113176 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