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_010936554.1 DET_RS04285 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_000011905.1:WP_010936554.1 Length = 365 Score = 184 bits (467), Expect = 3e-51 Identities = 135/365 (36%), Positives = 195/365 (53%), Gaps = 32/365 (8%) Query: 3 KVCVIEGDGIGKEVIPEAIKILNELGE-----FEIIKGEAGLECLKKYGNALPEDTIEKA 57 K+ V+ GDGIG EV+ E +K+LN + + FE G G C+ K G AL +T+ Sbjct: 4 KLTVLPGDGIGPEVMAEGLKVLNAVAKKYKHSFEYQYGLIGGCCIDKEGVALSPETLAMC 63 Query: 58 KEADIILFGAITSPKPGEVKNYKSP---IITLRKMFHLYANVRPINNFGIGQLIGKIADY 114 K++D +L A+ P+ + K P ++ LR+ L+AN+RP+ + + A Sbjct: 64 KKSDAVLLAAVGDPRFDDPKLPVHPEDGLLALRRGLGLFANIRPVK---VAPSLVNSAPI 120 Query: 115 EFLNAKNIDIVIIRENTEDLYVGRERLENDTAIAERVIT------RKGSERIIRFAFEYA 168 + K D + IRE T +Y + + T R T K ERI+R FE A Sbjct: 121 KAEIVKGTDFIFIRELTGGVYFAKPKKRWTTPSGIRKATDSMTYSEKEIERIVRVGFELA 180 Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEKFD 227 ++ +KK+ + KANVL ++ L+ ++ EI K Y +I + LVD+ AM LI P FD Sbjct: 181 -RSRKKKLVSVDKANVL-LSSRLWRQIVIEIAKDYPDITVEHILVDACAMKLILAPTYFD 238 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDKA-------LFEPVHGSAPDIAGKGI 280 VIVT NMFGDIL+DEAS L G +G+ PSA++ A L+EP+HGSAP IA + I Sbjct: 239 VIVTENMFGDILTDEASMLAGSMGMLPSASLAGIPAKGTKTFGLYEPIHGSAPTIAKQNI 298 Query: 281 ANPMASILSIAMLFDY-IGEKEKGDLIREAVKYCLINKKVTPDL----GGDLKTKDVGDE 335 ANP+A+ILSIAM+ Y G + + I AV L T D+ L T ++G + Sbjct: 299 ANPIATILSIAMMLRYSCGLETEAAEIEAAVDKVLAAGYATIDIFKEGNTKLGTAEMGSQ 358 Query: 336 ILNYI 340 I I Sbjct: 359 IAKII 363 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: 312 Number of extensions: 19 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: 365 Length adjustment: 29 Effective length of query: 318 Effective length of database: 336 Effective search space: 106848 Effective search space used: 106848 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 10 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