Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_028320142.1 H567_RS0102190 3-isopropylmalate dehydrogenase
Query= SwissProt::P9WKK9 (336 letters) >NCBI__GCF_000422285.1:WP_028320142.1 Length = 354 Score = 300 bits (767), Expect = 5e-86 Identities = 172/345 (49%), Positives = 218/345 (63%), Gaps = 16/345 (4%) Query: 3 LAIIAGDGIGPEVTAEAVKVLDAVVPGVQKT----SYDLGARRFHATGEVLPDSVVAELR 58 + +I GDG GPEV AE +K L+A T YDLG + G +LPDSV+ ELR Sbjct: 7 IGVIPGDGTGPEVVAEGLKALEAAGRKHDLTFDFKRYDLGGEAYLRDGTLLPDSVIHELR 66 Query: 59 NHDAILLGAIGDPSVPSGVLERGLLLRLRFELDHHINLRPARLYPGVASPLSGNP--GID 116 DAI LGAIG P V G+LER +LL+LRFELD +INLRP L+PGV +PL G ID Sbjct: 67 GMDAIFLGAIGHPGVKPGILEREVLLKLRFELDLYINLRPVVLHPGVDTPLMGKQPEDID 126 Query: 117 FVVVREGTEGPYTGNGGAIRVGTPNEVATEVSVNTAFGVRRVVADAFERARRRRK--HLT 174 FVVVRE +EG Y G GG + GT +EVA + SVNT GV R + AFE AR+R K H+T Sbjct: 127 FVVVRENSEGMYAGGGGFFKKGTADEVAIQESVNTRKGVERCIRYAFEYARKRNKGKHVT 186 Query: 175 LVHKTNVLTFAGGLWLRTVDEVGECYPDVEVAYQHVDAATIHMITDPGRFDVIVTDNLFG 234 L KTNVL F LW R +V + +PD+ YQHVDA + MI +P +FDVIVT NLFG Sbjct: 187 LCAKTNVLIFESDLWFRVFQDVAKDFPDIGTGYQHVDALCMWMIKNPEQFDVIVTGNLFG 246 Query: 235 DIITDLAAAVCGGIGLAASGNIDATRANPSMFEPVHGSAPDIAGQGIADPTAAIMSVALL 294 DIITD+ A + GG+G+AA GNI ++ +MFEP+ GSAP GQ +P AAI S +L Sbjct: 247 DIITDIGAIIQGGLGIAAGGNIHPGQS--AMFEPIGGSAPKYTGQNKINPMAAIGSAQML 304 Query: 295 LSHLGEHDAAARVDRAVEAHLA------TRGSERLATSDVGERIA 333 L +LG+ AAA + +A+ L+ G TS+VG+ +A Sbjct: 305 LEYLGKDKAAADIFQAIRKVLSQDLKSLEAGRMGYTTSEVGDLVA 349 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: 356 Number of extensions: 18 Number of successful extensions: 5 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 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