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_020563805.1 A3OW_RS0112640 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000372865.1:WP_020563805.1 Length = 432 Score = 149 bits (375), Expect = 2e-40 Identities = 119/375 (31%), Positives = 170/375 (45%), Gaps = 82/375 (21%) Query: 7 IEGDGIGKEVVPATIQVLEATGL-------PFEFVYAEAGDEVYKRTGKALPEETIETAL 59 IEGDG G ++ AT++VL+A ++ AG++ + LP+ T++ Sbjct: 33 IEGDGTGPDIWRATVRVLDAAVARSYSGRRKIHWLEIYAGEKSNRLFNTWLPDATVDACR 92 Query: 60 DCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVIVR 112 D + G G + V LR +LD Y +RPV+ ++GV RP+ +D VI R Sbjct: 93 DYLVSIKGPLTTPVGGGIRSLNVTLRQVLDLYVCLRPVRWFQGVPSPVKRPEAVDMVIFR 152 Query: 113 ENTEGLYKGIEAE-------------------------IDEGITIATRVITEKACERIFR 147 ENTE +Y GIE E E I + ++ + ER+ R Sbjct: 153 ENTEDIYAGIEFEQGSEDNRRFLQLLREHFPAQYAKIRFPETAGIGIKPVSREGTERLVR 212 Query: 148 FA--FNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAE-EYDD---------- 194 A F LA RK VT HK N++K T+G F+ Y +AE EY + Sbjct: 213 AAIDFALANRRKS------VTLVHKGNIMKFTEGAFRNWAYALAEREYAEQVYPWSRWER 266 Query: 195 ----------------------IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDG 232 I +D D ++T+P FDV+ T NL GD LSD Sbjct: 267 TKAASGEAAANKEQAEALAQGRILMKDGIADITLQQVLTRPDDFDVIATLNLNGDYLSDA 326 Query: 233 AAGTVGGLGLAPSANIGDEHG--LFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEY 290 A VGG+G+AP NI G +FE HG+AP A NP + ILS +MLRY+G Sbjct: 327 LAAQVGGIGIAPGGNINYSTGTAVFEATHGTAPKYADLDKVNPGSLILSGEMMLRYMGWT 386 Query: 291 EAADKVEKALEEVLA 305 EAAD + +A++ +A Sbjct: 387 EAADALIRAMDAAIA 401 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: 337 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 333 Length of database: 432 Length adjustment: 30 Effective length of query: 303 Effective length of database: 402 Effective search space: 121806 Effective search space used: 121806 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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