Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_012853863.1 TCUR_RS17470 3-isopropylmalate dehydrogenase
Query= SwissProt::P9WKK9 (336 letters) >NCBI__GCF_000024385.1:WP_012853863.1 Length = 353 Score = 428 bits (1100), Expect = e-124 Identities = 224/340 (65%), Positives = 263/340 (77%), Gaps = 7/340 (2%) Query: 1 MKLAIIAGDGIGPEVTAEAVKVLDAVVPG----VQKTSYDLGARRFHATGEVLPDSVVAE 56 ++LA+I GDGIGPEV AE +KVLDAV P +T+YDLGA R+H TGE LPDSV+ E Sbjct: 9 VRLAVIPGDGIGPEVVAEGLKVLDAVAPAHGLVFDRTTYDLGAARWHRTGETLPDSVLEE 68 Query: 57 LRNHDAILLGAIGDPSVPSGVLERGLLLRLRFELDHHINLRPARLYPGVASPLSG--NPG 114 LR D ILLGA+GDPSVPSGVLERGLLLRLRFELDH++NLRP +L+PGV +PL+ Sbjct: 69 LRGQDVILLGAVGDPSVPSGVLERGLLLRLRFELDHYVNLRPVKLFPGVKTPLADVTPDD 128 Query: 115 IDFVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFERARRR-RKHL 173 ID VVVREGTEGPYTG GG +R GTP EVAT+ SVNTA+GV RV+ AFE+A R RK L Sbjct: 129 IDMVVVREGTEGPYTGVGGVLRKGTPQEVATQESVNTAYGVERVIRYAFEQAAARPRKKL 188 Query: 174 TLVHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLF 233 TLVHK NVLTFAG L+ RT+ V YP V Y HVDAAT+ + +P RFDVIVTDNLF Sbjct: 189 TLVHKDNVLTFAGDLYQRTLKRVATEYPQVTTDYCHVDAATMFFVNNPQRFDVIVTDNLF 248 Query: 234 GDIITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVAL 293 GDIITD+ AA+ GGIGLAASGN++ R PSMFEPVHGSAPDIAGQ ADPTA I+SVA+ Sbjct: 249 GDIITDIGAAIAGGIGLAASGNVNPDRTAPSMFEPVHGSAPDIAGQAKADPTATILSVAM 308 Query: 294 LLSHLGEHDAAARVDRAVEAHLATRGSERLATSDVGERIA 333 LL+H+G +AA V++AV A LA RG+ AT +VG+ IA Sbjct: 309 LLNHIGATEAARAVEQAVSADLAERGTAVRATHEVGDAIA 348 Lambda K H 0.319 0.137 0.398 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: 399 Number of extensions: 21 Number of successful extensions: 4 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: 336 Length of database: 353 Length adjustment: 29 Effective length of query: 307 Effective length of database: 324 Effective search space: 99468 Effective search space used: 99468 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 (21.8 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