Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_011032593.1 MM_RS03355 3-isopropylmalate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000007065.1:WP_011032593.1 Length = 330 Score = 278 bits (712), Expect = 1e-79 Identities = 163/337 (48%), Positives = 218/337 (64%), Gaps = 17/337 (5%) Query: 3 KICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALDCD 62 ++ VIEGDGIG+EV+PA ++VL+A GL FE V E G ++RTG A+ EE +E C+ Sbjct: 2 RLAVIEGDGIGREVIPAAVEVLDAFGLEFEKVPLEIGYARWERTGTAMSEEDMEIIKSCN 61 Query: 63 AVLFGAAGETAAD-----VIVKLRHILDTYANIRPVKAYKGVKCL--RPDIDYVIVRENT 115 AVLFGA T D V++ +R LD YAN+RPVK GV + R D D++IVRENT Sbjct: 62 AVLFGAV-TTVPDPGYKSVLLTIRKELDLYANVRPVKPLSGVVGVSGRSDFDFIIVRENT 120 Query: 116 EGLYKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLK 175 EGLY GIE EI ++ RVIT K ERI +A LA++R GK+T HK+NVLK Sbjct: 121 EGLYSGIE-EIGHDLSWTKRVITRKGSERISEYACELAKKRS-----GKLTIVHKSNVLK 174 Query: 176 LTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAG 235 +D LF + + A Y ++ D +D+M +I P+ +DVVVT+NLFGDILSD A Sbjct: 175 -SDKLFLDVCRETASSYG-VEYGDMLVDSMAYSLIMHPEKYDVVVTTNLFGDILSDMCAA 232 Query: 236 TVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADK 295 VG LGL PSANIG ++ FEPVHGSAPDIAGK I+NP A IL ++L ++G+ EA Sbjct: 233 LVGSLGLVPSANIGKKYAFFEPVHGSAPDIAGKGISNPLAAILCVKMLLEWMGKPEAR-L 291 Query: 296 VEKALEEVLALGLTTPDLGGNLNTFEMAEEVAKRVRE 332 ++ A+ ++L + TPDLGG +T E+ VAK + + Sbjct: 292 IDAAIADLLQKKIITPDLGGRASTAEVGNAVAKYIMQ 328 Lambda K H 0.318 0.138 0.390 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: 302 Number of extensions: 13 Number of successful extensions: 7 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: 333 Length of database: 330 Length adjustment: 28 Effective length of query: 305 Effective length of database: 302 Effective search space: 92110 Effective search space used: 92110 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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