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_014027430.1 PYRFU_RS09335 isocitrate/isopropylmalate dehydrogenase family protein
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000223395.1:WP_014027430.1 Length = 349 Score = 298 bits (762), Expect = 2e-85 Identities = 172/336 (51%), Positives = 219/336 (65%), Gaps = 15/336 (4%) Query: 3 KICVIEGDGIGKEVVPATIQVLEAT----GLPFEFVYAEAGDEVYKRTGKALPEETIETA 58 + C+IEGDGIG EV AT++VLEA G+ FE V EAGDE KR G LPEET+ A Sbjct: 16 RFCLIEGDGIGPEVSRATLRVLEAVSKRFGIGFEPVLCEAGDEAAKRRGSPLPEETLRKA 75 Query: 59 LDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGV--KCLRPDIDYVIVRENTE 116 + VL G GETA +V+ LR L TYA IRP K GV +C +P +D VIVRE E Sbjct: 76 KEIGIVLKGPVGETAGEVVTVLRRELGTYAAIRPAKTLPGVSPRCGKP-LDVVIVRELLE 134 Query: 117 GLYKGIEAE--IDEGITIATRVITEKACERIFRFAFNLARERKKMGKEGKVTCAHKANVL 174 G+Y E + +A RV + + ER+ R A +AR G+ G V+ HKANVL Sbjct: 135 GVYVQTEYVDVVSNSFAVALRVASARETERVARLAARIAR-----GRRGIVSIIHKANVL 189 Query: 175 KLTDGLFKKIFYKVAEEYDDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAA 234 T GLF+ + +V EE + + E+YY+DA ++ P+ FDV++T NLFGDILSD AA Sbjct: 190 HGTCGLFRDVAKRVLEE-EGVVVEEYYVDAAAALLVRTPERFDVMLTPNLFGDILSDLAA 248 Query: 235 GTVGGLGLAPSANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAAD 294 G LGL+PSAN+GD+ G+FEPVHG+A DIAG IANPTA +L+A +ML +LG +AA Sbjct: 249 ELAGSLGLSPSANVGDKTGIFEPVHGAAFDIAGMGIANPTAMMLAAAMMLDWLGYRDAAR 308 Query: 295 KVEKALEEVLALGLTTPDLGGNLNTFEMAEEVAKRV 330 +EKA+E+ LA G TPDLGGNL T E AEEVAKR+ Sbjct: 309 AIEKAIEDALASGARTPDLGGNLKTMEFAEEVAKRI 344 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: 295 Number of extensions: 11 Number of successful extensions: 6 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: 349 Length adjustment: 29 Effective length of query: 304 Effective length of database: 320 Effective search space: 97280 Effective search space used: 97280 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