Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate WP_069661914.1 BCR25_RS01940 NADP-dependent isocitrate dehydrogenase
Query= curated2:O29627 (326 letters) >NCBI__GCF_001730305.1:WP_069661914.1 Length = 425 Score = 137 bits (345), Expect = 5e-37 Identities = 114/402 (28%), Positives = 179/402 (44%), Gaps = 79/402 (19%) Query: 4 IVVIPGDGIGKEVMEAAMLILE-------KLDLPFEYSYYDAGDEALEKYGKALPDETLE 56 I I GDGIG E+ +AA L+ + K + + AG++A + G LP+ETL Sbjct: 22 IPFIEGDGIGPEIWQAAKLVFDAAVNKAYKNERKVVWQEVLAGEKAFKMTGDWLPEETLT 81 Query: 57 ACRKSDAVLFGAA----GETAADVIVRLRRELGTFANVRPAKAIEGIEC--LYPGL-DIV 109 + + G G + V LR+EL + RP + EG+ +P L D++ Sbjct: 82 VIKDHLVAIKGPLTTPIGGGFRSLNVTLRQELDLYVCYRPVRYFEGVPSPLKHPELTDMM 141 Query: 110 VVRENTECLYMGFEFG----------------FG------DVTEAIRV--ITREASERIA 145 + RENTE +Y G EF FG T AI + +++E +ER+ Sbjct: 142 IFRENTEDIYAGIEFPAESLEAEKLITYLKTEFGIDKIRFPKTSAIGIKPVSKEGTERLV 201 Query: 146 RYAFELAKREGRKKVTALHKANVMKKTCGLFRDVCREVAK-----------DY------- 187 R A E A + RK VT +HK N+MK T G F+ +AK DY Sbjct: 202 RGAIEHALKHKRKSVTLVHKGNIMKFTEGGFKQWGYALAKTEFSDAVFTWEDYLKSKEEL 261 Query: 188 ---------------PEIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLV 232 ++ D D +++ P +DV+ T N+ GD +SD A V Sbjct: 262 GKTAADQQLAAAETAGKLIIKDRIADIFLQDILLHPTNYDVVATLNLNGDYISDALAAQV 321 Query: 233 GGLGLAPSANVGERT--AIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKK 290 GG+G+AP AN+ T IFE HG A + AG NP++++L+ ++ + G+ E ++ Sbjct: 322 GGIGIAPGANLNLETGHGIFEATHGTAPEFAGLNQLNPSSLLLSGALLFEYLGWFEVSRL 381 Query: 291 VEEAVEKTIKEGKKTPDLGGN------LKTMEFANEVASLLD 326 + E++E + T D L +F E+ L++ Sbjct: 382 IIESIEAALINRTVTKDFADQMEQATLLSCSDFGEELVRLIE 423 Lambda K H 0.321 0.139 0.399 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: 275 Number of extensions: 17 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 326 Length of database: 425 Length adjustment: 30 Effective length of query: 296 Effective length of database: 395 Effective search space: 116920 Effective search space used: 116920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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