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_012102496.1 CKL_RS10565 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >NCBI__GCF_000016505.1:WP_012102496.1 Length = 354 Score = 192 bits (487), Expect = 1e-53 Identities = 127/310 (40%), Positives = 186/310 (60%), Gaps = 20/310 (6%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELG-----EFEIIKGEAGLECLKKYGNALPEDTIEK 56 MK+ +I GDG+GKE+I + K+L +FE + G + + G LPE+TI+ Sbjct: 1 MKIAIIPGDGVGKEIIAQGKKVLKAAAHKYKFDFEYEEVLLGGSAIDEKGTPLPEETIKI 60 Query: 57 AKEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIGKIA 112 K +D +L GA+ PK PG ++ ++ ++ +RK ++AN+RP F + + Sbjct: 61 CKSSDAVLLGAVGGPKWDKLPGNLRP-EAGLLGIRKALGVFANLRPAILFPELKSASNLK 119 Query: 113 DYEFLNAKNIDIVIIRENTEDLYVGRERLENDTAIAERVITRKGS----ERIIRFAFEYA 168 E L + +DI+I+RE T Y G + N + T S +RI R +FE A Sbjct: 120 P-EVLG-EGLDIMIVRELTGGAYFGEKDRINVEGGQKAWDTISYSTFEIDRIARRSFEIA 177 Query: 169 IKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHYN-IEADDYLVDSTAMNLIKHPEKFD 227 K N KK++ I KANVL + L+ EV EI K Y+ +E + VD+ AM LIK+P +FD Sbjct: 178 RKRN-KKLTLIDKANVLE-SSKLWREVVAEIAKEYDDVELNYMYVDNAAMQLIKNPGQFD 235 Query: 228 VIVTTNMFGDILSDEASALIGGLGLAPSANIGDDK-ALFEPVHGSAPDIAGKGIANPMAS 286 VI+T NMFGDILSDEAS L G LG+ PSA++ +D L+EP+HGSAPDIAG+ ANP+ + Sbjct: 236 VILTENMFGDILSDEASMLTGSLGMLPSASVREDSFGLYEPIHGSAPDIAGQNKANPIGT 295 Query: 287 ILSIAMLFDY 296 ++SI+M+F Y Sbjct: 296 LMSISMMFKY 305 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: 23 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: 354 Length adjustment: 29 Effective length of query: 318 Effective length of database: 325 Effective search space: 103350 Effective search space used: 103350 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