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_041098001.1 SUTH_RS06440 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_000828635.1:WP_041098001.1 Length = 350 Score = 201 bits (512), Expect = 2e-56 Identities = 140/355 (39%), Positives = 204/355 (57%), Gaps = 27/355 (7%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELG-EFEIIKGEAGLECLKKYGNALPEDTIEKAKEA 60 MK+CV+ GDGIG E+I EA+++L L + E+ + G + G+ P+ T + A A Sbjct: 1 MKICVLPGDGIGPEIIAEAVRVLKALDLKIEMEEALLGGCAVDATGSPYPDATQKLALAA 60 Query: 61 DIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADYEFL 117 D +L GA+ P+ + P ++ +RK L+AN+RP L ++A+ L Sbjct: 61 DAVLLGAVGGPQWDNNPREQRPERGLLGIRKQLGLFANLRP------AILYPELANASTL 114 Query: 118 NAK---NIDIVIIRENTEDLYVGRER---LENDTAIAERVITRKGSE--RIIRFAFEYAI 169 + +DI+I+RE T D+Y G+ R + N + SE RI+R AFE A Sbjct: 115 KPEVVAGLDILIVRELTGDIYFGQPRGIEVRNGERFGFNTMHYTESEIRRILRVAFEAAK 174 Query: 170 KNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFDV 228 K NRK V + K NVL T L+ +V E + Y ++E LVD+ AM L+K+P++FDV Sbjct: 175 KRNRK-VCSVDKMNVLECTQ-LWRDVAIETGREYPDVELSHMLVDNAAMQLVKNPKQFDV 232 Query: 229 IVTTNMFGDILSDEASALIGGLGLAPSANI-GDDKALFEPVHGSAPDIAGKGIANPMASI 287 +VT NMFGDILSDEAS L G +G+ PSA++ ++K L+EP HGSAPDIAGKG+ANP+A+I Sbjct: 233 MVTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGVANPLATI 292 Query: 288 LSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL----GGDLKTKDVGDEIL 337 LS AM+ Y ++ I AVK L T D+ + T+ +GD +L Sbjct: 293 LSAAMMLRYTFANEDAAGRIETAVKKVLAQGFRTGDIYEPGMKKVGTRAMGDAVL 347 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: 322 Number of extensions: 14 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: 350 Length adjustment: 29 Effective length of query: 318 Effective length of database: 321 Effective search space: 102078 Effective search space used: 102078 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