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 Echvi_2062 Echvi_2062 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58991 (347 letters) >FitnessBrowser__Cola:Echvi_2062 Length = 353 Score = 210 bits (534), Expect = 5e-59 Identities = 135/361 (37%), Positives = 204/361 (56%), Gaps = 28/361 (7%) Query: 2 MKVCVIEGDGIGKEVIPEAIKILNELGEF--------EIIKGEAGLECLKKYGNALPEDT 53 M + ++ GDGIG EVI + +K++ +G+ E + G A ++ GN P++T Sbjct: 1 MNIALLPGDGIGPEVIEQTVKVVKAVGKKFGHTITFKEAVVGAAAIDAT---GNPYPDET 57 Query: 54 IEKAKEADIILFGAITSPK----PGEVKNYKSPIITLRKMFHLYANVRPINNFGIGQLIG 109 E +AD +LFGAI PK P + ++ +RK L++NVRP F LI Sbjct: 58 HEICLQADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLFSNVRP--TFTFPSLIH 115 Query: 110 KIADYEFLNAKNIDIVIIRENTEDLYVGRERLENDT---AIAERVITRKGSERIIRFAFE 166 K + + + D+V +RE T +Y G R N+ A V T++ R+ R FE Sbjct: 116 K-SPLKKERIEGTDLVFLRELTGGIYFGEPRGRNEQGTKAFDTNVYTKEEITRLARMGFE 174 Query: 167 YAIKNNRKKVSCIHKANVLRITDGLFLEVFNEIKKHY-NIEADDYLVDSTAMNLIKHPEK 225 +A K RK ++C+ KANVL T L+ E E++ Y +++ + VD+ AM LI+ P+ Sbjct: 175 FAQKR-RKLLTCVDKANVLA-TSRLWRETVQELEPEYPDVKVEYEFVDAVAMRLIQWPKA 232 Query: 226 FDVIVTTNMFGDILSDEASALIGGLGLAPSANIGDDKALFEPVHGSAPDIAGKGIANPMA 285 +DV++T N+FGDIL+DEAS + G +GL PSA++G D LFEP+HGS P AGK IANP+A Sbjct: 233 YDVLITENLFGDILTDEASVISGSMGLMPSASLGTDVKLFEPIHGSYPQAAGKDIANPLA 292 Query: 286 SILSIAMLFDYIGE-KEKGDLIREAVKYCLINKKVTPDLGGD---LKTKDVGDEILNYIR 341 ++LS AM+F+Y + K++ I + V L VT D+ + KT +VGD + I Sbjct: 293 TVLSAAMMFEYAFDLKDEAKAISDVVNLSLAEGVVTEDIAEESKPSKTSEVGDWLAAQIL 352 Query: 342 K 342 K Sbjct: 353 K 353 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: 18 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: 353 Length adjustment: 29 Effective length of query: 318 Effective length of database: 324 Effective search space: 103032 Effective search space used: 103032 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