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_083765277.1 HM1_RS06690 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000019165.1:WP_083765277.1 Length = 422 Score = 167 bits (424), Expect = 3e-46 Identities = 124/386 (32%), Positives = 183/386 (47%), Gaps = 66/386 (17%) Query: 7 IEGDGIGKEVVPATIQVLEAT-----GLPFEFVYAE--AGDEVYKRTGKALPEETIETAL 59 IEGDG G ++ A+ V +A G + E AG++ K LPEET+E Sbjct: 41 IEGDGTGPDIWRASQAVFDAAIEKAYGGQKRIAWMEVYAGEKAKKNFDTWLPEETVEAFQ 100 Query: 60 DCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC---LRPDIDYVIVR 112 + + G G + V LR ++D YA +RPV+ + GV +D VI R Sbjct: 101 EFRVGIKGPLTTPVGGGFRSLNVTLRQVMDLYACVRPVRYFNGVPSPVKTPEKVDMVIFR 160 Query: 113 ENTEGLYKGIEAE---------------------IDEGITIATRVITEKACERIFRFAFN 151 ENTE +Y G+E + + +G + + ++E +R+ R A Sbjct: 161 ENTEDVYAGLEWKAGTAEAQKAIEFFRNEMGVKILKDGTALGLKPVSEFGSKRLIRKAIQ 220 Query: 152 LARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAEE------------YDD----- 194 A + K+ VT HK N++K T+G FK Y++A E +D+ Sbjct: 221 YAIDNKRKS----VTLVHKGNIMKFTEGAFKDWGYELAAEEFAEQTISEAALWDEYNGKV 276 Query: 195 ----IKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGD 250 I +D D+M I+ +P +DV+ T+NL GD LSD A VGGLG+AP NI D Sbjct: 277 PEGKIVIKDRIADSMFQQILLRPDEYDVLATTNLNGDYLSDALAAQVGGLGIAPGGNISD 336 Query: 251 EHGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTT 310 + +FE HG+AP AG NP + ILS V+ML +LG EAAD + K L++ + + T Sbjct: 337 AYAVFEATHGTAPKYAGLDKVNPGSVILSGVMMLEHLGWQEAADLIVKGLQKAIEDKVVT 396 Query: 311 PDLGGNL------NTFEMAEEVAKRV 330 DL + T E A V +R+ Sbjct: 397 YDLARQIAGAREVKTSEFARAVIERM 422 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: 347 Number of extensions: 18 Number of successful extensions: 6 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: 422 Length adjustment: 30 Effective length of query: 303 Effective length of database: 392 Effective search space: 118776 Effective search space used: 118776 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 10 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