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 Echvi_4068 Echvi_4068 isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__Cola:Echvi_4068 Length = 487 Score = 224 bits (571), Expect = 3e-63 Identities = 129/317 (40%), Positives = 187/317 (58%), Gaps = 10/317 (3%) Query: 3 KICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETI-----ET 57 KI V GDGIG E++ AT+++LEA G E E G++VY + + E ET Sbjct: 6 KITVAYGDGIGPEIMKATLEILEAAGAQIEPEVIEIGEQVYLKGISSGIEPKAWDSLRET 65 Query: 58 ALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKG-VKCLRPDIDYVIVRENTE 116 + + + G + V R L YAN+RP KAY ++ P+ D VIVREN E Sbjct: 66 KIFLKSPITTPQGGGFKSLNVTTRKTLGLYANVRPCKAYSPYIRTHFPETDMVIVRENEE 125 Query: 117 GLYKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKL 176 LY GIE + + ++I+ E+I R+AF A++ + KVTC K N++KL Sbjct: 126 DLYAGIEHRQTDDVYQCLKLISRPGSEKIIRYAFEYAKKYNRK----KVTCMTKDNIMKL 181 Query: 177 TDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGT 236 DGLF K+F VA+EY +I+A+ ID I KP++FDV+VT NL+GDI+SD AA Sbjct: 182 ADGLFHKVFNDVAKEYPEIEADHKIIDIGTALIADKPEMFDVIVTLNLYGDIISDVAAQI 241 Query: 237 VGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKV 296 G +GL S+N+G++ +FE +HGSAPDIAG+ IANP+ + A++ML ++G+ E A+KV Sbjct: 242 TGSVGLGGSSNVGEDVAMFEAIHGSAPDIAGQNIANPSGLLNGAIMMLVHIGQPEVAEKV 301 Query: 297 EKALEEVLALGLTTPDL 313 A + L G+ T D+ Sbjct: 302 SNAWMKTLEDGIHTGDI 318 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: 419 Number of extensions: 26 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: 333 Length of database: 487 Length adjustment: 31 Effective length of query: 302 Effective length of database: 456 Effective search space: 137712 Effective search space used: 137712 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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