Align isocitrate dehydrogenase (NAD+) subunit 2; EC 1.1.1.41 (characterized)
to candidate N515DRAFT_1138 N515DRAFT_1138 isocitrate dehydrogenase (NAD+)
Query= CharProtDB::CH_125980 (378 letters) >FitnessBrowser__Dyella79:N515DRAFT_1138 Length = 338 Score = 315 bits (807), Expect = 1e-90 Identities = 162/335 (48%), Positives = 224/335 (66%), Gaps = 5/335 (1%) Query: 47 TVTMIAGDGIGPEIAQSVERIFKAAKVPIEWERVKVYPI-LKNGTTTIPDDAKESVRKNK 105 T+ +I GDGIGPEI ++ R+ A + +E V + L+ +P D +++ ++ Sbjct: 4 TIAVIPGDGIGPEIMKATLRVLDALDCGLSYEFVDAGMVALEKHGDLLPKDTLDAIARHT 63 Query: 106 VALKGPLATPIGKGHVSMNLTLRRTFGLFANVRPCVSITGYKTPYDNVNTVLIRENTEGE 165 +ALKGPL TPIG G S+N+TLRR F L+ANVRP +S G K ++N++ + +RENTEG Sbjct: 64 IALKGPLTTPIGGGFTSINVTLRRHFDLYANVRPAISFPGTKARFENIDIITVRENTEGA 123 Query: 166 Y--SGIEHEVIPGVVQSIKLITRAASERVIRYAFQYARQTGKNNITVVHKATIMRMADGL 223 Y G V S+ TR S R+++YAF+ ARQ G+ IT VHKA IM+ + GL Sbjct: 124 YLSEGQTLSEDGEVATSMVRNTRKGSTRIVKYAFEMARQKGRKKITAVHKANIMKTSSGL 183 Query: 224 FLECAKELAPEYPDIELREEILDNACLKIVTDPVPYNNTVMVMPNLYGDIVSDMCAGLIG 283 FL A+E+A EYPDIE E I+DN C+++V P ++ V+V NL+GDI+SD+CAGL+G Sbjct: 184 FLNVAREVAKEYPDIEFNEMIVDNTCMQLVMKPEQFD--VIVTTNLFGDILSDLCAGLVG 241 Query: 284 GLGLTPSGNIGNQASIFEAVHGTAPDIAGKGLANPTALLLSSVMMLKHMNLNDYAKRIES 343 GLGL P NIG A+IFEAVHG+APDIAGKG+ANP ALLL++ ML H+ + D ++ + Sbjct: 242 GLGLAPGDNIGAGAAIFEAVHGSAPDIAGKGIANPCALLLAAADMLDHLGMADKGNKVRA 301 Query: 344 AIFDTLANNPDARTKDLGGKSNNVQYTDAIISKLK 378 AI DTL N+ DA T DLGGK N + DAI+ ++K Sbjct: 302 AIRDTLTNDRDAVTPDLGGKGNTDSFGDAIVKRVK 336 Lambda K H 0.317 0.133 0.381 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: 365 Number of extensions: 13 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: 378 Length of database: 338 Length adjustment: 29 Effective length of query: 349 Effective length of database: 309 Effective search space: 107841 Effective search space used: 107841 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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