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_014448976.1 LFE_RS03940 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000284315.1:WP_014448976.1 Length = 336 Score = 239 bits (610), Expect = 7e-68 Identities = 138/332 (41%), Positives = 190/332 (57%), Gaps = 9/332 (2%) Query: 2 HKICVIEGDGIGKEVVPATIQVLEATGLPFEFVYAEAGDEVYKRTGKALPEETIETALDC 61 H I ++ G+G G E+ A +V++ +G+ + Y E G + K G LPE+TI++ Sbjct: 4 HVITMLPGEGTGPEICEAVRRVIDHSGVDITWEYEEIGLDCLKEHGTLLPEKTIKSIAKN 63 Query: 62 DAVLFGAA----GETAADVIVKLRHILDTYANIRPVKAYKGVKCLRPDIDYVIVRENTEG 117 + G G V LR + D YAN+RP K +K ID + RENTE Sbjct: 64 KIAIKGPTTTPVGTGHKSANVTLRKMFDLYANVRPAKLIPVLKRPWDKIDILSFRENTED 123 Query: 118 LYKGIEAEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVLKLT 177 Y IE + + + +VIT RI FAF AR + K+ C HKAN++K+T Sbjct: 124 SYAAIEHMVSDEVAQCLKVITWPGSIRIAEFAFKWARANNRK----KMQCVHKANIMKMT 179 Query: 178 DGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTV 237 DGLF + F +VA+ Y DI AED +D +M ++ P FD +V NL+GDILSD AG V Sbjct: 180 DGLFLEAFREVAKNYPDIVAEDIIVDNCSMQLVRNPGQFDCLVLPNLYGDILSDLCAGLV 239 Query: 238 GGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVE 297 GGLG AP ANIGD +FE VHGSAP AG K NP+A +LS V+ML++L E+EAA ++E Sbjct: 240 GGLGFAPGANIGDNCSIFEAVHGSAPKYAGMKKVNPSAVLLSGVMMLKWLNEHEAATRIE 299 Query: 298 KALEEVLALGL-TTPDLGGNLNTFEMAEEVAK 328 K +++VLA T D GG +T E A+ + K Sbjct: 300 KGVDKVLAEAKHLTYDAGGTASTDEYADAIIK 331 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: 304 Number of extensions: 13 Number of successful extensions: 3 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: 336 Length adjustment: 28 Effective length of query: 305 Effective length of database: 308 Effective search space: 93940 Effective search space used: 93940 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 Jul 25 2024. The underlying query database was built on Jul 25 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