Align homoisocitrate dehydrogenase (EC 1.1.1.87) (characterized)
to candidate CCNA_00193 CCNA_00193 3-isopropylmalate dehydrogenase
Query= BRENDA::Q5SIJ1 (334 letters) >FitnessBrowser__Caulo:CCNA_00193 Length = 350 Score = 213 bits (542), Expect = 6e-60 Identities = 145/350 (41%), Positives = 197/350 (56%), Gaps = 26/350 (7%) Query: 5 ICLIEGDGIGHEVIPAARRVLEATGLPLEFVEAEAGWETFERRGTSVPEETVEKILSCHA 64 + L+ GDGIG EV RRV A L+ EA G +++ GT + +E E+ L+ A Sbjct: 4 LLLLPGDGIGPEVCAQVRRVAAALTPDLKVDEALYGGASYDTHGTPLTDEVREQALASDA 63 Query: 65 TLFGAATSPT-----RKVPGFFGAIRYLRRRLDLYANVRPA--------KSRPVPGSRPG 111 L GA P R + G + LR+ +D++AN+RPA S P G Sbjct: 64 VLMGAVGGPKWADAPRHLRPEAGLLN-LRKAMDVFANLRPAYCFEALAGASSLKPELVSG 122 Query: 112 VDLVIVRENTEGLYVEQERRYLDVAIADA------VISKKASERIGRAALRIAEGRPRKT 165 +D++ VRE G+Y Q R D+A V + ER+GR A +A GR K Sbjct: 123 LDIMFVRELVGGVYFGQPRGIEDLADGQKKGFDTQVYTTSEIERVGRVAFELARGRTNK- 181 Query: 166 LHIAHKANVLPLTQGLFLDTVKEV-AKDFPLVNVQDIIVDNCAMQLVMRPERFDVIVTTN 224 +H A K+NV+ + L+ + E+ A+++P V ++ I+ DNCAMQLV P++FDVIVT N Sbjct: 182 VHSAEKSNVME-SGLLWKQVITELHAREYPDVQLEHILADNCAMQLVRAPKQFDVIVTDN 240 Query: 225 LLGDILSDLAAGLVGGLGLAPSGNIG--DTTAVFEPVHGSAPDIAGKGIANPTAAILSAA 282 L GDILSD AA L G LG+ PS +G ++EP+HGSAPDIAGKG+ANP AAILS Sbjct: 241 LFGDILSDAAAMLTGSLGMLPSAALGAPGKPGLYEPIHGSAPDIAGKGLANPLAAILSFE 300 Query: 283 MMLDY-LGEKEAAKRVEKAVDLVLERGPRTPDLGGDATTEAFTEAVVEAL 331 M L + L + EAA + AV L+ G RT DLGG TT +AV+ AL Sbjct: 301 MALRWSLKQTEAADALLAAVKAALDNGARTRDLGGSLTTTQMGDAVLAAL 350 Lambda K H 0.319 0.137 0.391 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: 300 Number of extensions: 20 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: 334 Length of database: 350 Length adjustment: 29 Effective length of query: 305 Effective length of database: 321 Effective search space: 97905 Effective search space used: 97905 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