Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_017598162.1 D471_RS0108155 3-isopropylmalate dehydrogenase
Query= SwissProt::P9WKK9 (336 letters) >NCBI__GCF_000341125.1:WP_017598162.1 Length = 354 Score = 420 bits (1079), Expect = e-122 Identities = 220/343 (64%), Positives = 258/343 (75%), Gaps = 9/343 (2%) Query: 1 MKLAIIAGDGIGPEVTAEAVKVLDAVVP----GVQKTSYDLGARRFHATGEVLPDSVVAE 56 + LA+I GDGIGPEV E +KVL+AV P ++ T Y+LGA+ +H TGE LPDSV E Sbjct: 6 VNLAVIPGDGIGPEVVGEGLKVLEAVAPQHDLAIEATEYELGAKLWHRTGETLPDSVEDE 65 Query: 57 LRNHDAILLGAIGDPSVPSGVLERGLLLRLRFELDHHINLRPARLYPGVASPLSG--NPG 114 LR H+AILLGA+GDPSVPSGVLERGLLLRLRF+ DH++NLRP RL+PGV SPL+G Sbjct: 66 LREHEAILLGAVGDPSVPSGVLERGLLLRLRFDFDHYVNLRPVRLFPGVDSPLAGVSPED 125 Query: 115 IDFVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFERAR-RRRKHL 173 ID +VVREGTEGPY G GG +R GTP+E+AT+ SVNT FGV RVV AF +A R RK L Sbjct: 126 IDMLVVREGTEGPYAGAGGVLRKGTPHEIATQDSVNTRFGVERVVRYAFAKAAVRPRKKL 185 Query: 174 TLVHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLF 233 TLVHK NVLTFAG LW R V EVG YP V V Y HVDAA + + P RFDV+VTDNLF Sbjct: 186 TLVHKDNVLTFAGDLWQRVVREVGAEYPQVSVDYCHVDAAAMFFVNQPARFDVVVTDNLF 245 Query: 234 GDIITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVAL 293 GDIITD+ AAV GGIGLAASGN++ PSMFEPVHGSAPDIAGQG ADPTA ++SVA Sbjct: 246 GDIITDIGAAVTGGIGLAASGNVNPDNTFPSMFEPVHGSAPDIAGQGKADPTATVLSVAT 305 Query: 294 LLSHLGEHDAAARVDRAVEAHLATR--GSERLATSDVGERIAA 334 +L HLG +AA R++ AV A L TR G +TS +G+ +AA Sbjct: 306 MLDHLGVPEAARRIEGAVAADLKTRAQGGAARSTSQIGDDLAA 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: 415 Number of extensions: 19 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: 354 Length adjustment: 29 Effective length of query: 307 Effective length of database: 325 Effective search space: 99775 Effective search space used: 99775 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