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 AO353_20635 AO353_20635 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20635 Length = 360 Score = 196 bits (498), Expect = 8e-55 Identities = 131/363 (36%), Positives = 206/363 (56%), Gaps = 32/363 (8%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 ++ ++ GDGIG E++ EA+K+L + FE+ G + K+G L ++T+ +A Sbjct: 4 QILILPGDGIGPEIMTEAVKVLELANDKFALDFELSHDVIGGAAIDKHGVPLADETLARA 63 Query: 58 KEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADY 114 + AD +L GA+ PK ++ P ++ +R L+ N+RP L ++A+ Sbjct: 64 RAADAVLLGAVGGPKWDTIERDIRPERGLLKIRAQLGLFGNLRP------AILYPQLAEA 117 Query: 115 EFLNAK---NIDIVIIRENTEDLYVGRER----LENDTAIAERVITRKGSE--RIIRFAF 165 L A+ +DI+I+RE T +Y G R LEN A + SE RI R F Sbjct: 118 SSLKAEIVAGLDILIVRELTGGIYFGAPRGVRELENGERQAYDTLPYSESEIRRIARVGF 177 Query: 166 EYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPE 224 + A + KK+ + KANVL + L+ E+ ++ K Y ++E VD+ AM L++ P+ Sbjct: 178 DMA-RVRGKKLCSVDKANVLASSQ-LWREIVEQVAKDYPDVELSHMYVDNAAMQLVRAPK 235 Query: 225 KFDVIVTTNMFGDILSDEASALIGGLGLAPSANI-GDDKALFEPVHGSAPDIAGKGIANP 283 +FDVIVT N+FGDILSDEAS L G +G+ PSA++ ++K ++EP HGSAPDIAGKGIANP Sbjct: 236 QFDVIVTDNLFGDILSDEASMLTGSIGMLPSASLDANNKGMYEPCHGSAPDIAGKGIANP 295 Query: 284 MASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGG----DLKTKDVGDEILN 338 +A+ILS++M+ Y + D I +AV L T D+ + T+++GD ++ Sbjct: 296 LATILSVSMMLRYSFNQLVAADAIEKAVSLVLDQGLRTGDIWSPGCVKVGTQEMGDAVVA 355 Query: 339 YIR 341 +R Sbjct: 356 ALR 358 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: 296 Number of extensions: 13 Number of successful extensions: 5 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: 360 Length adjustment: 29 Effective length of query: 318 Effective length of database: 331 Effective search space: 105258 Effective search space used: 105258 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