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 WP_011386420.1 AMB_RS20570 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_000009985.1:WP_011386420.1 Length = 369 Score = 194 bits (494), Expect = 2e-54 Identities = 136/346 (39%), Positives = 195/346 (56%), Gaps = 32/346 (9%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELG-----EFEIIKGEAGLECLKKYGNALPEDTIEKA 57 K+ ++ GDGIG EV+ + +I++ +G EFEI +G G +G P +T+E A Sbjct: 5 KLLILPGDGIGVEVMAQVRRIIDWMGRKRKIEFEITEGLLGGAAYDVHGTPYPAETLEAA 64 Query: 58 KEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADY 114 AD +L GA+ PK ++ K P ++ +RK L+AN+RP ++ +AD Sbjct: 65 LAADAVLLGAVGGPKWDDLPFDKKPERGLLGIRKDMGLFANLRPAT------VLEALADA 118 Query: 115 EFLNAK---NIDIVIIRENTEDLYVGRERLENDTAIAER------VITRKGSERIIRFAF 165 L A+ +DI+I+RE T LY G+ R + R V T +RI R AF Sbjct: 119 STLKAEVVSGLDIMILRELTGGLYFGQPRGIDTLPDGTRKGYNTLVYTTPEIQRIGRVAF 178 Query: 166 EYAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPE 224 + A K N KK+ + KANVL T E+ K+ + ++E VD+ AM L+++P+ Sbjct: 179 DLARKRN-KKLCSVDKANVLECTVLWREEMIKLQKEEFPDVELTHMYVDNAAMQLVRNPK 237 Query: 225 KFDVIVTTNMFGDILSDEASALIGGLGLAPSANIGD------DKALFEPVHGSAPDIAGK 278 +FDV+VT NMFGDILSD A+ L G LG+ PSA++G+ KAL+EPVHGSAPDIAGK Sbjct: 238 QFDVMVTENMFGDILSDCAAMLTGSLGMLPSASLGEADAQGKRKALYEPVHGSAPDIAGK 297 Query: 279 GIANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL 323 +ANP+A+I+S AM Y + DLI AVK L T D+ Sbjct: 298 DMANPLATIMSFAMCLRYSFDMAAEADLIETAVKNVLKGGLRTADI 343 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: 325 Number of extensions: 14 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: 369 Length adjustment: 29 Effective length of query: 318 Effective length of database: 340 Effective search space: 108120 Effective search space used: 108120 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