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 HSERO_RS07015 HSERO_RS07015 isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__HerbieS:HSERO_RS07015 Length = 418 Score = 149 bits (376), Expect = 1e-40 Identities = 115/365 (31%), Positives = 172/365 (47%), Gaps = 63/365 (17%) Query: 7 IEGDGIGKEVVPATIQVLEAT-------GLPFEFVYAEAGDEVYKRTGKA--LPEETIET 57 I GDG+G +V P ++V+ A ++ AG++ + G LPEET+ Sbjct: 34 IVGDGVGVDVTPVMLKVVNAAVEKAYGGARKIHWMEIYAGEKATRLYGPDVWLPEETLAV 93 Query: 58 ALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVI 110 + G G + V +R LD Y +RPV+ +KGV P+ D VI Sbjct: 94 LKKYLVAIKGPLSTPVGGGIRSLNVAMRQQLDLYVCLRPVRYFKGVPSPLREPEKTDMVI 153 Query: 111 VRENTEGLYKGIE-----AEIDEGITIATRV------------------ITEKACERIFR 147 REN+E +Y GIE E+++ I + TR ++ + ER+ R Sbjct: 154 FRENSEDIYAGIEWAAGTPEVNKLIDLLTREMGVKKLRFPESSALGIKPVSREGTERLVR 213 Query: 148 FAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVA------EEYDD------- 194 A A + K VT HK N++K T+G F+ Y +A E DD Sbjct: 214 QAIQYAIDHDKPS----VTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGPWMRLK 269 Query: 195 -------IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSAN 247 I +D DA ++ +P + V+ T NL GD +SD A VGG+G+AP AN Sbjct: 270 NPKTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIAPGAN 329 Query: 248 IGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALG 307 + D +FE HG+AP AGK NP ++ILSA +MLR++G EAAD + A+++ ++ Sbjct: 330 MSDSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMGWIEAADLIISAMQKSVSSK 389 Query: 308 LTTPD 312 T D Sbjct: 390 RVTYD 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: 303 Number of extensions: 15 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 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