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 BPHYT_RS15730 BPHYT_RS15730 isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__BFirm:BPHYT_RS15730 Length = 418 Score = 156 bits (394), Expect = 1e-42 Identities = 122/368 (33%), Positives = 176/368 (47%), Gaps = 69/368 (18%) Query: 7 IEGDGIGKEVVPATIQVLEATGLPFEFVYAE----------AGDEVYKRTGKA--LPEET 54 IEGDG G ++ P I+V++A E YA AG++ K G LPEET Sbjct: 34 IEGDGTGLDITPVMIKVVDAA---VEKAYAGKKKIHWMEIYAGEKSTKVYGPDVWLPEET 90 Query: 55 I----ETALDCDAVLFGAAGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-ID 107 + E + L G + V LR LD Y +RPV+ +KGV P+ + Sbjct: 91 LQVLKEYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCLRPVQYFKGVPSPVREPEKTN 150 Query: 108 YVIVRENTEGLYKGIE--AEIDE------------GIT---------IATRVITEKACER 144 VI REN+E +Y GIE AE ++ G+ I + ++ + ER Sbjct: 151 MVIFRENSEDIYAGIEWPAESEQAKKVIKFLREEMGVKKIRFPDTSGIGIKPVSREGTER 210 Query: 145 IFRFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEEY------------ 192 + R A A + ++ VT HK N++K T+G F+ Y +A++ Sbjct: 211 LVRKAIQYAIDNERRS----VTLVHKGNIMKFTEGAFRDYGYALAQKEFAAELIDGGPWM 266 Query: 193 --------DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAP 244 DI +D DA I+ +P +DV+ T NL GD +SD A VGG+G+AP Sbjct: 267 KIKNPKTGGDIVLKDVIADAFLQQILLRPAEYDVIATLNLNGDYVSDALAAQVGGIGIAP 326 Query: 245 SANIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVL 304 AN+ D +FE HG+AP AGK NP + ILSA +MLR+LG EAAD + K++E+ + Sbjct: 327 GANMSDSVAMFEATHGTAPKYAGKDYVNPGSEILSAEMMLRHLGWTEAADLIIKSMEKSI 386 Query: 305 ALGLTTPD 312 T D Sbjct: 387 LQKRVTYD 394 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: 22 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: 333 Length of database: 418 Length adjustment: 30 Effective length of query: 303 Effective length of database: 388 Effective search space: 117564 Effective search space used: 117564 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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