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 HSERO_RS16500 HSERO_RS16500 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__HerbieS:HSERO_RS16500 Length = 356 Score = 207 bits (527), Expect = 3e-58 Identities = 139/357 (38%), Positives = 208/357 (58%), Gaps = 26/357 (7%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELGE-FEIIKGEAGLECLKKYGNALPEDTIEKAKEA 60 MK+ ++ GDGIG E++ EA+++LN L E FE+ G + +G+ LP+ T++ AKEA Sbjct: 1 MKIAILPGDGIGPEIVNEAVRVLNALDEKFEMETAPVGGAGYEAHGHPLPDGTLKLAKEA 60 Query: 61 DIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADYEFL 117 D ILFGA+ K +++ P I+ LRK L+AN RP + +L G + L Sbjct: 61 DAILFGAVGDWKYDKLERALRPEQAILGLRKHLQLFANFRPAICYP--ELTGASSLKPEL 118 Query: 118 NAKNIDIVIIRENTEDLYVGRERLENDTAIAERVITRKGSE----------RIIRFAFEY 167 A N+DI+I+RE D+Y G+ R + R+G + RI AF+ Sbjct: 119 VA-NLDILIVRELNGDIYFGQPRGMREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQA 177 Query: 168 AIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKF 226 A K K++ + KANVL T + ++ E+ K Y ++E VD+ AM L+K P+ F Sbjct: 178 AAKRG-KRLCSVDKANVLE-TFQFWKDIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNF 235 Query: 227 DVIVTTNMFGDILSDEASALIGGLGLAPSANI-GDDKALFEPVHGSAPDIAGKGIANPMA 285 DVIVT NMFGDILSD A+ L G +G+ PSA++ ++K L+EP HGSAPDIAG+GIANP+A Sbjct: 236 DVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGRGIANPLA 295 Query: 286 SILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGD----LKTKDVGDEIL 337 +ILS AM+ + + + E+ D I AVK L T D+ + + T+ +G+ ++ Sbjct: 296 TILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTADIYEEGCTKVNTQQMGEAVV 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: 344 Number of extensions: 21 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: 347 Length of database: 356 Length adjustment: 29 Effective length of query: 318 Effective length of database: 327 Effective search space: 103986 Effective search space used: 103986 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