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 PP_4011 PP_4011 isocitrate dehydrogenase, NADP(+)-specific
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__Putida:PP_4011 Length = 418 Score = 159 bits (401), Expect = 2e-43 Identities = 124/384 (32%), Positives = 179/384 (46%), Gaps = 72/384 (18%) Query: 7 IEGDGIGKEVVPATIQVLEAT---------GLPFEFVYA-EAGDEVYKRTGKALPEETIE 56 IEGDGIG +V P I+V++A + + VYA E +VY + LP+ET++ Sbjct: 34 IEGDGIGVDVSPVMIKVVDAAVQKAYGGKRKIAWMEVYAGEKATQVYDQD-TWLPQETLD 92 Query: 57 TALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRP-DIDYV 109 D + G G + V LR LD Y +RPV ++GV +P D+D V Sbjct: 93 AVRDYVVSIKGPLTTPVGGGIRSLNVALRQQLDLYVCLRPVLWFQGVPSPVKKPGDVDMV 152 Query: 110 IVRENTEGLYKGIE-----------------------AEIDEGITIATRVITEKACERIF 146 I REN+E +Y GIE D+ I + ++++ +R+ Sbjct: 153 IFRENSEDIYAGIEWKAGSPEANKVIKFLKEEMGVTKIRFDQDCGIGVKPVSKEGTKRLV 212 Query: 147 RFAFNLARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEEY-------------- 192 R A + + +T HK N++K T+G FK Y+VA + Sbjct: 213 RKALQYVVDNDRES----LTLVHKGNIMKFTEGAFKDWGYEVARDEFGAELLDGGPWMKF 268 Query: 193 ------DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSA 246 ++ +D DAM I+ +P +DV+ T NL GD LSD A VGG+G+AP A Sbjct: 269 KNPKTGREVIVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGA 328 Query: 247 NIGDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLAL 306 N+ D +FE HG+AP AG+ NP + ILSA +MLR++G EAAD + K +A Sbjct: 329 NLSDTVAMFEATHGTAPKYAGQDKVNPGSVILSAEMMLRHMGWTEAADLIIKGTNGAIAA 388 Query: 307 GLTTPDLGGNLNTFEMAEEVAKRV 330 T D FE E AK V Sbjct: 389 KTVTYD-------FERLMEGAKLV 405 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: 310 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 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