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 GFF1981 Psest_2024 isocitrate dehydrogenase, NADP-dependent, prokaryotic type
Query= SwissProt::Q58130 (333 letters) >FitnessBrowser__psRCH2:GFF1981 Length = 418 Score = 164 bits (414), Expect = 5e-45 Identities = 126/364 (34%), Positives = 177/364 (48%), Gaps = 61/364 (16%) Query: 7 IEGDGIGKEVVPATIQVLEAT---------GLPFEFVYA-EAGDEVYKRTGKALPEETIE 56 IEGDGIG ++ P I+V++A + + +YA E +VY + LP+ET+E Sbjct: 34 IEGDGIGVDISPVMIKVVDAAVQKAYGGQRKIAWMEIYAGEKATQVYDQD-TWLPKETLE 92 Query: 57 TALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRP-DIDYV 109 D + G G + V LR LD Y RPV+ + GV +P D+D V Sbjct: 93 AVRDYVVSIKGPLTTPVGGGIRSLNVALRQELDLYVCQRPVRWFTGVPSPVKKPGDVDMV 152 Query: 110 IVRENTEGLYKGIEAEIDEGITIATRVI---TEKACERIFRFAFNLARERKKMGKEG--- 163 I REN+E +Y G+E + G A +VI TE+ + RF N K + EG Sbjct: 153 IFRENSEDIYAGVEWKA--GSPEAEKVIKFLTEEMGVKKIRFTENCGIGIKPVSLEGTKR 210 Query: 164 ---------------KVTCAHKANVLKLTDGLFKKIFYKVAEEY---------------- 192 VT HK N++K T+G FK+ Y+VA + Sbjct: 211 LVRKALQYAVDNDRSSVTIVHKGNIMKFTEGAFKEWGYEVARDEFGAELLDGGPWMQFKN 270 Query: 193 ----DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANI 248 +I +D DAM I+ +P +DV+ T NL GD LSD A VGG+G+AP AN+ Sbjct: 271 PNTGKNIVVKDAIADAMLQQILLRPAEYDVIATLNLNGDYLSDALAAEVGGIGIAPGANL 330 Query: 249 GDEHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGL 308 D +FE HG+AP AG+ NP + ILSA +MLR++G EAAD + K+ E +A Sbjct: 331 SDTVAMFEATHGTAPKYAGQDKVNPGSLILSAEMMLRHMGWVEAADLIIKSTESAIAAKT 390 Query: 309 TTPD 312 T D Sbjct: 391 VTYD 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: 313 Number of extensions: 19 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