Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_015739918.1 ADEG_RS09915 3-isopropylmalate dehydrogenase
Query= SwissProt::P9WKK9 (336 letters) >NCBI__GCF_000024605.1:WP_015739918.1 Length = 353 Score = 324 bits (831), Expect = 2e-93 Identities = 182/349 (52%), Positives = 231/349 (66%), Gaps = 16/349 (4%) Query: 2 KLAIIAGDGIGPEVTAEAVKVLDAVVP----GVQKTSYDLGARRFHATGEVLPDSVVAEL 57 ++A+I GDG GPE E +KVL+AV + YD G R+ TGE LPDS + EL Sbjct: 4 RIAVIPGDGTGPEQVREGLKVLEAVAQLEGFKYETVVYDFGGERYLRTGETLPDSAIEEL 63 Query: 58 RNHDAILLGAIGDPSVPSGVLERGLLLRLRFELDHHINLRPARLYPGVASPLS--GNPGI 115 + AI LGAIG P V G+LE+G+LLRLRFELD +INLRP +LYPGV +PL G I Sbjct: 64 KQFHAIYLGAIGHPDVKPGILEKGILLRLRFELDQYINLRPVKLYPGVETPLKDKGPEDI 123 Query: 116 DFVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFE--RARRRRKHL 173 DFVVVRE TEG Y G GG +R GT +EVA ++S+NT GV R V AFE R R ++K + Sbjct: 124 DFVVVRENTEGLYCGAGGFLRRGTKDEVALQISINTYKGVERCVRYAFEYCRKRNKKKKV 183 Query: 174 TLVHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLF 233 TL KTNVLT+A LW R VGE YPD+ Y HVDA + M+ +P FDVIVTDN+F Sbjct: 184 TLCGKTNVLTYAFDLWERVFHAVGEEYPDITRDYAHVDAICMWMVKNPEWFDVIVTDNMF 243 Query: 234 GDIITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVAL 293 GDIITDL A + GG+G+AA NI+ SMFEP+ GSAP AG+ +P AAI+++A+ Sbjct: 244 GDIITDLGAIIQGGLGIAAGANINP--QGVSMFEPIGGSAPKYAGKNQINPLAAILALAM 301 Query: 294 LLSHLGEHDAAARVDRAVE----AHLATRGSERL--ATSDVGERIAAAL 336 LL HLGE AAAR++RAV+ HL + + R+ TS+VG+ + L Sbjct: 302 LLEHLGEERAAARIERAVQEVCSKHLKSLAAGRMGYTTSEVGDLVVRYL 350 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: 337 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: 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 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