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_018125754.1 B149_RS0113780 NADP-dependent isocitrate dehydrogenase
Query= SwissProt::Q58130 (333 letters) >NCBI__GCF_000375485.1:WP_018125754.1 Length = 379 Score = 186 bits (471), Expect = 1e-51 Identities = 124/356 (34%), Positives = 180/356 (50%), Gaps = 49/356 (13%) Query: 7 IEGDGIGKEVVPATIQVLEAT-------GLPFEFVYAEAGDEVYKRTGKALPEETIETAL 59 IEGDGIG EV + VL+A ++V AG++ + TG+ LP+ T++ Sbjct: 9 IEGDGIGPEVWASARPVLDAAMDKAYGGSNSLDWVELLAGEKAFAETGEYLPQTTMDALA 68 Query: 60 DCDAVLFGAAGETAA----DVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVIVR 112 + + G G + V +R D YA IRPV+ + G++ P+ +D V+ R Sbjct: 69 KAELAMKGPLGTPVGKGFRSLNVTMRQAFDLYACIRPVRHFAGIESPVKHPERVDMVVFR 128 Query: 113 ENTEGLYKGIE--------------------AEIDEGITIATRVITEKACERIFRFAFNL 152 ENTE +Y GIE A++D + + +TEK +R+ R A Sbjct: 129 ENTEDVYAGIEYASGSAEAKKLIAFLRDELGADVDPSAGVGIKPMTEKGSKRLVRRAIEF 188 Query: 153 ARERKKMGKEGKVTCAHKANVLKLTDGLFKKIFYKVAE-----------EYDDIKAEDYY 201 A G+E VT HK N++K T+G F+ Y+VAE E + +D Sbjct: 189 AARE---GRES-VTLVHKGNIMKTTEGAFRAWGYEVAEQEFAGTCVMEGEEGKVVVKDRI 244 Query: 202 IDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSANIGDEHGLFEPVHGS 261 DAM + +P+ + VV TSNL GD +SD A VGGLGLAP N+GD +FE HG+ Sbjct: 245 ADAMFQECLMRPEQYSVVATSNLNGDYISDALAAQVGGLGLAPGVNMGDTLAMFEATHGT 304 Query: 262 APDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLALGLTTPDLGGNL 317 AP IAGK +ANP + ILS ++L + G EAA+ V ++E+ LA T DL + Sbjct: 305 APTIAGKDMANPGSLILSGAMLLDHAGFGEAAELVRGSVEKALAARKVTVDLASQI 360 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: 302 Number of extensions: 19 Number of successful extensions: 7 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: 379 Length adjustment: 29 Effective length of query: 304 Effective length of database: 350 Effective search space: 106400 Effective search space used: 106400 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: 49 (23.5 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