Align isocitrate dehydrogenase (NAD+) (subunit 2/2) (EC 1.1.1.41) (characterized)
to candidate N515DRAFT_1138 N515DRAFT_1138 isocitrate dehydrogenase (NAD+)
Query= BRENDA::P50213 (366 letters) >FitnessBrowser__Dyella79:N515DRAFT_1138 Length = 338 Score = 307 bits (787), Expect = 2e-88 Identities = 164/337 (48%), Positives = 224/337 (66%), Gaps = 8/337 (2%) Query: 32 QTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWE--ERNVTAIQGPGGKWMIPSEAKESMD 89 +T+ +IPGDGIGPEI A +++ DA + +E + + A++ G ++P + +++ Sbjct: 3 KTIAVIPGDGIGPEIMKATLRVLDALDCGLSYEFVDAGMVALEKHGD--LLPKDTLDAIA 60 Query: 90 KNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENT 149 ++ + LKGPL TPI G S+N+ LR+ FDLYANVRP +S G K + +++I+T+RENT Sbjct: 61 RHTIALKGPLTTPIGGGFTSINVTLRRHFDLYANVRPAISFPGTKARFENIDIITVRENT 120 Query: 150 EGEY-SGIEHVIVDG-VVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMS 207 EG Y S + + DG V S+ T S RI ++AFE AR R +TAVHKANIM+ S Sbjct: 121 EGAYLSEGQTLSEDGEVATSMVRNTRKGSTRIVKYAFEMARQKGRKKITAVHKANIMKTS 180 Query: 208 DGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLI 267 GLFL REVA+ DI+FNEM +D C+ +V P QFDV+V NL+GDILSDLCAGL+ Sbjct: 181 SGLFLNVAREVAKEYPDIEFNEMIVDNTCMQLVMKPEQFDVIVTTNLFGDILSDLCAGLV 240 Query: 268 GGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARI 327 GGLG+ P NIGA G AIFE+VHG+APDIAGK +ANP ALLL+A ML H+G+ D ++ Sbjct: 241 GGLGLAPGDNIGA-GAAIFEAVHGSAPDIAGKGIANPCALLLAAADMLDHLGMADKGNKV 299 Query: 328 EAACFATI-KDGKSLTKDLGGNAKCSDFTEEICRRVK 363 AA T+ D ++T DLGG F + I +RVK Sbjct: 300 RAAIRDTLTNDRDAVTPDLGGKGNTDSFGDAIVKRVK 336 Lambda K H 0.319 0.136 0.403 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: 348 Number of extensions: 17 Number of successful extensions: 5 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: 366 Length of database: 338 Length adjustment: 29 Effective length of query: 337 Effective length of database: 309 Effective search space: 104133 Effective search space used: 104133 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 (21.7 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