Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_015798938.1 AFER_RS07950 3-isopropylmalate dehydrogenase
Query= SwissProt::P9WKK9 (336 letters) >NCBI__GCF_000023265.1:WP_015798938.1 Length = 342 Score = 340 bits (872), Expect = 3e-98 Identities = 186/316 (58%), Positives = 226/316 (71%), Gaps = 9/316 (2%) Query: 2 KLAIIAGDGIGPEVTAEAVKVLDAVVPGVQKTSYDLGARRFHATGEVLPDSVVAELRNHD 61 ++A+I GDGIGPEV EA+KV++A ++ + +LGA + ATGEVL D+ + LR+HD Sbjct: 4 RVAVIGGDGIGPEVIREALKVVEATGVVLETRAVELGAAHYLATGEVLDDATLEFLRSHD 63 Query: 62 AILLGAIG----DPSVPSGVLERGLLLRLRFELDHHINLRPAR-LYPGVASPLSGNPGID 116 AILLGAIG VP GVLERGLLLRLRFELD ++N RP R + P V D Sbjct: 64 AILLGAIGPAIGSTEVPPGVLERGLLLRLRFELDLYVNERPFRTIDPSVTVT---RREAD 120 Query: 117 FVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFERARRR-RKHLTL 175 FVV+RE TEGPY G GG + GT +EVA + S+NT GV RVV AFERAR R RKHLTL Sbjct: 121 FVVIRENTEGPYAGEGGFLYRGTAHEVAQQGSLNTRHGVERVVRYAFERARSRPRKHLTL 180 Query: 176 VHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLFGD 235 VHKTNVLT+AG LW RT EV YPDV AY HVDAA+I+++ DPGR+DVIVTDNLFGD Sbjct: 181 VHKTNVLTYAGDLWSRTFAEVAAEYPDVMTAYNHVDAASIYLVEDPGRYDVIVTDNLFGD 240 Query: 236 IITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVALLL 295 I+TDLAAAV GIG AAS N++ R PS+FEPVHG+A D G A+P AAI S +L Sbjct: 241 ILTDLAAAVTQGIGYAASANLNPARTGPSLFEPVHGAAHDRVGTNTANPWAAIRSAGAML 300 Query: 296 SHLGEHDAAARVDRAV 311 LGEH+AA+R++ A+ Sbjct: 301 EFLGEHEAASRIEAAL 316 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: 351 Number of extensions: 12 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: 342 Length adjustment: 28 Effective length of query: 308 Effective length of database: 314 Effective search space: 96712 Effective search space used: 96712 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