Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; Beta-IPM dehydrogenase; EC 1.1.1.85 (characterized)
to candidate WP_086510509.1 BZY95_RS13880 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::P50455 (337 letters) >NCBI__GCF_002151265.1:WP_086510509.1 Length = 363 Score = 191 bits (485), Expect = 2e-53 Identities = 115/347 (33%), Positives = 180/347 (51%), Gaps = 23/347 (6%) Query: 4 TVALIQGDGIGPEIVSKSKRILAKINELYSLPIEYIEVEAGDRALARYGEALPKDSLKII 63 T+ ++ GD IG EIV + + E L I++ + G +AL +G +P +L+ + Sbjct: 7 TLGVLNGDDIGHEIVPAAVEVAQAAAERCGLVIDWRHMPLGRKALDEFGTTMPDGTLETL 66 Query: 64 DKADIILKGPVG-------ESAADVVVKLRQIYDMYANIRPAKSIPGIDTKYGNVDILIV 116 D + GP+G E A + LR+ +D++AN+RP +S P I Y ++D++IV Sbjct: 67 STFDGFILGPIGHREYPKVEGAINPHPILRKHFDLFANVRPTRSYPDIGCIYDDIDLVIV 126 Query: 117 RENTEDLYKGFEHIVSDG-------VAVGMKIITRFASERIAKVGLNFALRRRKKVTCVH 169 REN E + G V + +++ITR S ++A L A R K++T VH Sbjct: 127 RENNEGFQPDRNVVAGSGEFRPTEDVTISVRVITREGSRKVATAALELARARNKRLTVVH 186 Query: 170 KANVMRITDGLFAEACRSVLKG--KVEYSEMYVDAAAANLVRNPQMFDVIVTENVYGDIL 227 K V ++ G+F E C + V+ E VD A +L+RNPQ +DV+VT N++GDIL Sbjct: 187 KNTVYKLGCGMFVEECYKAAEAYPDVKVDEAIVDTFAMHLIRNPQQYDVVVTTNMFGDIL 246 Query: 228 SDEASQIAGSLGIAPSANIG-DKKALFEPVHGAAFDIAGKNIGNPTAFLLSVSMMYE--- 283 +DEA+ + G LG+AP IG A+ + HG+A DIAG + NP A + S M+ E Sbjct: 247 TDEAAGLVGGLGMAPGLCIGRGNMAMAQATHGSAPDIAGTGLANPYAMIESTRMLIEWLG 306 Query: 284 RMYELSNDDRYIKASRALENAIYLVYKERKALTPDVGGNATTDDLIN 330 R +EL A+ + I + + TPD+ G D++N Sbjct: 307 RRHELPGAQ---AAAALMAKGIQAALADPRTRTPDIRGQGRLSDMVN 350 Lambda K H 0.318 0.137 0.380 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: 268 Number of extensions: 16 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: 337 Length of database: 363 Length adjustment: 29 Effective length of query: 308 Effective length of database: 334 Effective search space: 102872 Effective search space used: 102872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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