Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; EC 1.1.1.85; Beta-IPM dehydrogenase (uncharacterized)
to candidate N515DRAFT_1138 N515DRAFT_1138 isocitrate dehydrogenase (NAD+)
Query= curated2:O29627 (326 letters) >FitnessBrowser__Dyella79:N515DRAFT_1138 Length = 338 Score = 303 bits (776), Expect = 4e-87 Identities = 162/329 (49%), Positives = 214/329 (65%), Gaps = 9/329 (2%) Query: 2 KKIVVIPGDGIGKEVMEAAMLILEKLDLPFEYSYYDAGDEALEKYGKALPDETLEACRKS 61 K I VIPGDGIG E+M+A + +L+ LD Y + DAG ALEK+G LP +TL+A + Sbjct: 3 KTIAVIPGDGIGPEIMKATLRVLDALDCGLSYEFVDAGMVALEKHGDLLPKDTLDAIARH 62 Query: 62 DAVLFGAA----GETAADVIVRLRRELGTFANVRPAKAIEGIECLYPGLDIVVVRENTEC 117 L G G + V LRR +ANVRPA + G + + +DI+ VRENTE Sbjct: 63 TIALKGPLTTPIGGGFTSINVTLRRHFDLYANVRPAISFPGTKARFENIDIITVRENTEG 122 Query: 118 LYMGFEFGF---GDVTEAIRVITREASERIARYAFELAKREGRKKVTALHKANVMKKTCG 174 Y+ G+V ++ TR+ S RI +YAFE+A+++GRKK+TA+HKAN+MK + G Sbjct: 123 AYLSEGQTLSEDGEVATSMVRNTRKGSTRIVKYAFEMARQKGRKKITAVHKANIMKTSSG 182 Query: 175 LFRDVCREVAKDYPEIQYNDYYIDAACMYLVMDPFRFDVIVTTNMFGDIVSDLAAGLVGG 234 LF +V REVAK+YP+I++N+ +D CM LVM P +FDVIVTTN+FGDI+SDL AGLVGG Sbjct: 183 LFLNVAREVAKEYPDIEFNEMIVDNTCMQLVMKPEQFDVIVTTNLFGDILSDLCAGLVGG 242 Query: 235 LGLAPSANVGERTAIFEPVHGAAFDIAGKGIANPTAMILTACMMLRHFGYVEEAKKVEEA 294 LGLAP N+G AIFE VHG+A DIAGKGIANP A++L A ML H G ++ KV A Sbjct: 243 LGLAPGDNIGAGAAIFEAVHGSAPDIAGKGIANPCALLLAAADMLDHLGMADKGNKVRAA 302 Query: 295 VEKTIKEGKK--TPDLGGNLKTMEFANEV 321 + T+ + TPDLGG T F + + Sbjct: 303 IRDTLTNDRDAVTPDLGGKGNTDSFGDAI 331 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: 316 Number of extensions: 11 Number of successful extensions: 4 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: 326 Length of database: 338 Length adjustment: 28 Effective length of query: 298 Effective length of database: 310 Effective search space: 92380 Effective search space used: 92380 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 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