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 GFF2936 PGA1_c29830 3-isopropylmalate dehydrogenase LeuB
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Phaeo:GFF2936 Length = 367 Score = 195 bits (495), Expect = 2e-54 Identities = 134/363 (36%), Positives = 197/363 (54%), Gaps = 37/363 (10%) Query: 4 VCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKAK 58 + ++ GDGIG EV+ E K+++ GE F++ + G +G L ++T+EKA+ Sbjct: 6 ILILPGDGIGPEVMAEVRKVISWYGEKRDLQFDVSEDLVGGAAYDVHGKPLADETMEKAQ 65 Query: 59 EADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADYE 115 E D +L GA+ PK ++ P ++ LRK LY+N+RP Q +AD+ Sbjct: 66 EVDAVLLGAVGGPKYDDLDFSVKPERGLLRLRKEMDLYSNLRP------AQCFDALADFS 119 Query: 116 FLN---AKNIDIVIIRENTEDLYVGR-----ERLENDTAIAERVITRKGSERIIRFAFEY 167 L +DI+I+RE T +Y G E I + T ER R AFE Sbjct: 120 SLKKDIVAGLDIMIVRELTSGVYFGEPRGIFEEGNERVGINTQRYTESEIERAARSAFEL 179 Query: 168 AIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKF 226 A++ N KK+ + KANV+ + L+ EV + Y +E D+ AM L++ P++F Sbjct: 180 AMRRN-KKLCSMEKANVME-SGILWREVVTRVAADYPEVELSHMYADNGAMQLVRAPKQF 237 Query: 227 DVIVTTNMFGDILSDEASALIGGLGLAPSANI------GDDKALFEPVHGSAPDIAGKGI 280 DVI+T N+FGDILSD A+ L G LG+ PSA++ G KAL+EPVHGSAPDIAG+G Sbjct: 238 DVILTDNLFGDILSDCAAMLTGSLGMLPSASLGAPMANGRPKALYEPVHGSAPDIAGQGK 297 Query: 281 ANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDLGGD-----LKTKDVGD 334 ANP+A ILS AM Y + + D + AV+ L + T DL G+ + T ++GD Sbjct: 298 ANPIACILSFAMALRYSFDQGSEADRLETAVEKVLADGHRTGDLLGEEGVSPISTSEMGD 357 Query: 335 EIL 337 I+ Sbjct: 358 VII 360 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: 348 Number of extensions: 20 Number of successful extensions: 7 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: 367 Length adjustment: 29 Effective length of query: 318 Effective length of database: 338 Effective search space: 107484 Effective search space used: 107484 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