Align Homoisocitrate dehydrogenase; HICDH; Homo(2)-isocitrate/homo(3)-isocitrate dehydrogenase; Isohomocitrate dehydrogenase; IHDH; NAD-dependent threo-isohomocitrate dehydrogenase; EC 1.1.1.87; EC 1.1.1.- (characterized)
to candidate Ac3H11_1528 3-isopropylmalate dehydrogenase (EC 1.1.1.85)
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1528 Length = 357 Score = 214 bits (546), Expect = 2e-60 Identities = 146/357 (40%), Positives = 207/357 (57%), Gaps = 26/357 (7%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELG-EFEIIKGEAGLECLKKYGNALPEDTIEKAKEA 60 MK+ V+ GDGIG E++ EA+K+L L +FE+ G + +G+ LPE T++ AKEA Sbjct: 1 MKIAVLPGDGIGTEIVAEAVKVLKALDLKFEMESALVGGAAYEAHGHPLPESTLKLAKEA 60 Query: 61 DIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADYEFL 117 D ILFGA+ K ++ P I+ LRK L+AN RP + QL+G + L Sbjct: 61 DAILFGAVGDWKYDKLDRPLRPEQAILGLRKNLGLFANFRPAICYE--QLVGASSLKPEL 118 Query: 118 NAKNIDIVIIRENTEDLYVGRERLEN----------DTAIAERVITRKGSERIIRFAFEY 167 A +DI+IIRE T D+Y G+ R + A +R ERI AF+ Sbjct: 119 IA-GLDILIIRELTGDIYFGQPRGRRVATDGHFPGAEEAFDTMRYSRPEIERIAHVAFQA 177 Query: 168 AIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKF 226 A K N KKV+ + KANVL T + +V ++ K Y ++E VD+ AM L+K P+ F Sbjct: 178 ARKRN-KKVTSVDKANVLE-TFQFWKDVVTDVHKEYPDVELQHMYVDNAAMQLVKAPKAF 235 Query: 227 DVIVTTNMFGDILSDEASALIGGLGLAPSANI-GDDKALFEPVHGSAPDIAGKGIANPMA 285 DV+VT NMFGDILSDEAS L G +G+ PSA++ ++ L+EP HGSAPDIAGKG+ANP+A Sbjct: 236 DVVVTGNMFGDILSDEASMLTGSIGMLPSASLNSSNQGLYEPSHGSAPDIAGKGVANPLA 295 Query: 286 SILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGDLKTK----DVGDEIL 337 +ILS AM+ + + ++ I AV+ L TPD+ + TK +GD ++ Sbjct: 296 TILSAAMMLRFSLNQEAAAQRIEAAVQKVLAQGLRTPDIYSEGTTKVGTAQMGDAVV 352 Lambda K H 0.319 0.140 0.397 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: 323 Number of extensions: 20 Number of successful extensions: 8 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: 347 Length of database: 357 Length adjustment: 29 Effective length of query: 318 Effective length of database: 328 Effective search space: 104304 Effective search space used: 104304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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