Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden. |
We have performed NucPred and PredictNLS predictions for a number of fully sequenced eukaryotic organisms. More precisely, we have used sets of proteins from the EBI which are thought to be complete proteomes (but may not be, of course). We also include the pseudo-proteome of all 98716 eukaryotic sequences in UniProt Knowledgebase - for which quality functional annotations are often available. This is a simple interface to view and analyse the results. With it you can answer questions such as: "Which proteins are confidently predicted to have a nuclear function by NucPred but are not currently known to be nuclear?" You can also focus your interests on proteins associated with human diseases. When you click on the link in the NucPred score column you can see the NucPred prediction in detail and can then easily send the sequence to other prediction servers (PredictNLS and PSORT II). |
UniProt accession | UniProt ID | UniProt description | NucPred score | Predict- NLS | PSORT II | TMHMM #helices | UniProt annotation for subcellular location | Uniprot GO cellular component | OMIM | PDB | sequence length |
P51826 UniProt NPD GO | AFF3_HUMAN | AF4/FMR2 family member 3 (Protein LAF-4) (Lymphoid nuclear protein related to AF4) | 1.00 | - | nuc | 0 | Nucleus | nucleus [TAS] | 601464 | 1227 | |
P35187 UniProt NPD GO | SGS1_YEAST | ATP-dependent helicase SGS1 (EC 3.6.1.-) (Helicase TPS1) | 1.00 | - | nuc | 0 | Nucleus | nucleolus [IDA] RecQ helicase-Topo III complex [IPI] | 1D8B | 1447 | |
Q6PL18 UniProt NPD GO | ATAD2_HUMAN | ATPase family AAA domain-containing protein 2 | 1.00 | + | nuc | 0 | 1390 | ||||
Q61315 UniProt NPD GO | APC_MOUSE | Adenomatous polyposis coli protein (Protein APC) (mAPC) | 1.00 | - | nuc | 0 | cytoplasm [IDA] nucleus [IDA] | 1VJ6 | 2845 | ||
P55196 UniProt NPD GO | AFAD_HUMAN | Afadin (Protein AF-6) | 1.00 | + | nuc | 0 | Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs | intercellular junction [TAS] | 159559 | 1XZ9 | 1816 |
O35889 UniProt NPD GO | AFAD_RAT | Afadin (Protein Af-6) | 1.00 | + | nuc | 0 | Cell membrane; cell-cell junction; adherens junction. Not found at cell-matrix AJs | 1829 | |||
Q5U312 UniProt NPD GO | RAI14_RAT | Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ... | 1.00 | - | nuc | 0 | Cytoplasm. Associated with the cortical actin cytoskeleton structures in terminal web and cell-cell ... | 978 | |||
Q9P0K7 UniProt NPD GO | RAI14_HUMAN | Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ... | 1.00 | - | nuc | 0 | Cytoplasm. Associated with the cortical actin cytoskeleton structures in terminal web and cell-cell ... | 606586 | 980 | ||
Q9EP71 UniProt NPD GO | RAI14_MOUSE | Ankycorbin (Ankyrin repeat and coiled-coil structure-containing protein) (Retinoic acid-induced prot ... | 1.00 | - | nuc | 0 | Cytoplasm (By similarity). Associated with the cortical actin cytoskeleton structures in terminal we ... | mitochondrion [IDA] | 979 | ||
P46013 UniProt NPD GO | KI67_HUMAN | Antigen KI-67 | 1.00 | + | nuc | 0 | Nucleus. Predominantly localized in the G1 phase in the perinucleolar region, in the later phases it ... | 176741 | 2AFF | 3256 | |
Q8R4I1 UniProt NPD GO | ATX7_MOUSE | Ataxin-7 (Spinocerebellar ataxia type 7 protein homolog) | 1.00 | - | nuc | 0 | Nucleus (By similarity). Nucleus; nucleolus (By similarity). Nucleus; nuclear matrix (By similarity) ... | cytoplasm [IDA] nucleus [IDA] | 867 | ||
Q8WXX7 UniProt NPD GO | AUTS2_HUMAN | Autism susceptibility gene 2 protein | 1.00 | + | nuc | 0 | 607270 | 1259 | |||
O54952 UniProt NPD GO | BRCA1_RAT | Breast cancer type 1 susceptibility protein homolog | 1.00 | - | nuc | 0 | Nucleus (Potential) | 1L0B | 1817 | ||
Q9NRL2 UniProt NPD GO | BAZ1A_HUMAN | Bromodomain adjacent to zinc finger domain protein 1A (ATP-utilizing chromatin assembly and remodeli ... | 1.00 | + | nuc | 0 | Nucleus. May target the CHRAC complex to heterochromatin | 605680 | 1556 | ||
Q921C3 UniProt NPD GO | BRWD1_MOUSE | Bromodomain and WD repeat domain-containing protein 1 (WD repeat protein 9) | 1.00 | + | nuc | 0 | Cytoplasm. Nucleus | nucleus [IDA] | 2304 | ||
Q4R8Y1 UniProt NPD GO | BRDT_MACFA | Bromodomain testis-specific protein | 1.00 | + | nuc | 0 | Nucleus (Probable) | 947 | |||
Q58F21 UniProt NPD GO | BRDT_HUMAN | Bromodomain testis-specific protein (RING3-like protein) | 1.00 | + | nuc | 0 | Nucleus (Probable) | 602144 | 947 | ||
Q91Y44 UniProt NPD GO | BRDT_MOUSE | Bromodomain testis-specific protein (RING3-like protein) (Bromodomain-containing female sterile home ... | 1.00 | + | nuc | 0 | Nucleus (Probable) | nucleus [IDA] | 956 | ||
Q32S26 UniProt NPD GO | BRD2_BOVIN | Bromodomain-containing protein 2 | 1.00 | + | nuc | 0 | Nucleus (Potential) | 803 | |||
Q5TJG6 UniProt NPD GO | BRD2_CANFA | Bromodomain-containing protein 2 | 1.00 | + | nuc | 0 | Nucleus (Potential) | 803 | |||
P25440 UniProt NPD GO | BRD2_HUMAN | Bromodomain-containing protein 2 (Protein RING3) (O27.1.1) | 1.00 | + | nuc | 0 | Nucleus (Potential) | 601540 | 1X0J | 801 | |
O60885 UniProt NPD GO | BRD4_HUMAN | Bromodomain-containing protein 4 (HUNK1 protein) | 1.00 | + | nuc | 0 | Nucleus (By similarity) | 608749 | 1362 | ||
Q9ESU6 UniProt NPD GO | BRD4_MOUSE | Bromodomain-containing protein 4 (Mitotic chromosome-associated protein) (MCAP) | 1.00 | + | nuc | 0 | Nucleus | 1400 | |||
Q6NXW6 UniProt NPD GO | RAD17_MOUSE | Cell cycle checkpoint protein RAD17 | 1.00 | - | nuc | 0 | Nucleus. Phosphorylated form redistributes to discrete nuclear foci upon DNA damage (By similarity) | 688 | |||
Q69ZA1 UniProt NPD GO | CD2L5_MOUSE | Cell division cycle 2-like protein kinase 5 (EC 2.7.11.22) (CDC2-related protein kinase 5) | 1.00 | + | nuc | 0 | 1511 | ||||
Q14004 UniProt NPD GO | CD2L5_HUMAN | Cell division cycle 2-like protein kinase 5 (EC 2.7.11.22) (CDC2-related protein kinase 5) (Cholines ... | 1.00 | + | nuc | 0 | 603309 | 1512 | |||
Q9NYV4 UniProt NPD GO | CD2L7_HUMAN | Cell division cycle 2-related protein kinase 7 (EC 2.7.11.22) (CDC2-related protein kinase 7) (Cdc2- ... | 1.00 | - | nuc | 0 | Nucleus (Probable) | nucleus [IDA] | 1490 | ||
Q8IX12 UniProt NPD GO | CCAR1_HUMAN | Cell division cycle and apoptosis regulator protein 1 (Cell cycle and apoptosis regulatory protein 1 ... | 1.00 | + | nuc | 0 | Cytoplasm; perinuclear region | 1150 | |||
Q03188 UniProt NPD GO | CENPC_HUMAN | Centromere protein C 1 (CENP-C) (Centromere autoantigen C) | 1.00 | + | nuc | 0 | Nucleus | kinetochore [TAS] | 117141 | 943 | |
P49452 UniProt NPD GO | CENPC_MOUSE | Centromere protein C 1 (CENP-C) (Centromere autoantigen C) | 1.00 | + | nuc | 0 | Nucleus | 906 | |||
Q5VT06 UniProt NPD GO | CEP35_HUMAN | Centrosome-associated protein 350 (Centrosome-associated protein of 350 kDa) | 1.00 | + | nuc | 0 | Centrosome. Spindle. Associated with mitotic spindles. Nucleus. Nuclear, in discrete foci. Associate ... | 2COZ | 3117 | ||
Q13111 UniProt NPD GO | CAF1A_HUMAN | Chromatin assembly factor 1 subunit A (CAF-1 subunit A) (Chromatin assembly factor I p150 subunit) ( ... | 1.00 | + | nuc | 0 | Nucleus. DNA replication foci | chromatin assembly complex [TAS] | 601246 | 938 | |
Q6BKL0 UniProt NPD GO | EAF7_DEBHA | Chromatin modification-related protein EAF7 | 1.00 | - | nuc | 0 | Nucleus (By similarity) | 323 | |||
Q756L0 UniProt NPD GO | VID21_ASHGO | Chromatin modification-related protein VID21 | 1.00 | - | nuc | 0 | Nucleus (Probable) | 957 | |||
O14646 UniProt NPD GO | CHD1_HUMAN | Chromodomain-helicase-DNA-binding protein 1 (EC 3.6.1.-) (ATP-dependent helicase CHD1) (CHD-1) | 1.00 | - | nuc | 0 | Nucleus | 602118 | 2B2Y | 1709 | |
P40201 UniProt NPD GO | CHD1_MOUSE | Chromodomain-helicase-DNA-binding protein 1 (EC 3.6.1.-) (ATP-dependent helicase CHD1) (CHD-1) | 1.00 | - | nuc | 0 | Nucleus | nucleus [NAS] | 1711 | ||
O14647 UniProt NPD GO | CHD2_HUMAN | Chromodomain-helicase-DNA-binding protein 2 (EC 3.6.1.-) (ATP-dependent helicase CHD2) (CHD-2) | 1.00 | + | nuc | 0 | Nucleus (By similarity) | 602119 | 1739 | ||
Q3L8U1 UniProt NPD GO | CHD9_HUMAN | Chromodomain-helicase-DNA-binding protein 9 (EC 3.6.1.-) (ATP-dependent helicase CHD9) (CHD-9) (Chro ... | 1.00 | + | nuc | 0 | Cytoplasm. Nucleus | 2897 | |||
Q8BYH8 UniProt NPD GO | CHD9_MOUSE | Chromodomain-helicase-DNA-binding protein 9 (EC 3.6.1.-) (ATP-dependent helicase CHD9) (CHD-9) (Pero ... | 1.00 | + | nuc | 0 | Cytoplasm (By similarity). Nucleus (By similarity) | 2885 | |||
Q9DF50 UniProt NPD GO | CLSPN_XENLA | Claspin (xClaspin) | 1.00 | + | nuc | 0 | Nucleus (By similarity) | 1285 | |||
Q9C103 UniProt NPD GO | EME1_SCHPO | Crossover junction endonuclease eme1 (EC 3.1.22.-) (Essential meiotic endonuclease 1) | 1.00 | + | nuc | 0 | Nucleus | Holliday junction resolvase complex [TAS] | 738 | ||
Q05080 UniProt NPD GO | CYK2_YEAST | Cytokinesis 2 protein | 1.00 | - | nuc | 0 | contractile ring (sensu Saccharomyces) [IDA] | 669 | |||
Q9SR66 UniProt NPD GO | DML2_ARATH | DEMETER-like protein 2 (EC 3.2.2.-) | 1.00 | + | nuc | 0 | Nucleus (Potential) | 1309 | |||
Q9JIC3 UniProt NPD GO | DCR1A_MOUSE | DNA cross-link repair 1A protein | 1.00 | - | nuc | 0 | Nucleus (By similarity). In some cells it may be found in typically 1 or 2 discrete nuclear aggregat ... | 1026 | |||
P51892 UniProt NPD GO | DNL1_XENLA | DNA ligase 1 (EC 6.5.1.1) (DNA ligase I) (Polydeoxyribonucleotide synthase [ATP] 1) | 1.00 | - | nuc | 0 | Nucleus | 1070 | |||
Q61493 UniProt NPD GO | DPOLZ_MOUSE | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) (Seizure-related protein 4) | 1.00 | + | nuc | 0 | Nucleus (Potential) | 3122 | |||
O60673 UniProt NPD GO | DPOLZ_HUMAN | DNA polymerase zeta catalytic subunit (EC 2.7.7.7) (hREV3) | 1.00 | + | nuc | 0 | Nucleus (Potential) | 602776 | 3130 | ||
Q8TDM6 UniProt NPD GO | DLG5_HUMAN | Discs large homolog 5 (Placenta and prostate DLG) (Discs large protein P-dlg) | 1.00 | - | nuc | 0 | Cell membrane; cell-cell junction; peripheral membrane protein. Localized at sites of cell-cell cont ... | cytoplasm [TAS] plasma membrane [NAS] | 604090 | 1UIT | 1809 |
Q752Q3 UniProt NPD GO | EPL1_ASHGO | Enhancer of polycomb-like protein 1 | 1.00 | - | nuc | 0 | Nucleus (By similarity) | 742 | |||
Q6FLZ0 UniProt NPD GO | EPL1_CANGA | Enhancer of polycomb-like protein 1 | 1.00 | + | nuc | 0 | Nucleus (By similarity) | 821 |
You are viewing entries 1 to 50 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .
If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022The authors also look forward to your comments and suggestions. |
You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper. |
NucPred score threshold | Specificity | Sensitivity |
see above | fraction of proteins predicted to be nuclear that actually are nuclear | fraction of true nuclear proteins that are predicted (coverage) |
0.10 | 0.45 | 0.88 |
0.20 | 0.52 | 0.83 |
0.30 | 0.57 | 0.77 |
0.40 | 0.63 | 0.69 |
0.50 | 0.70 | 0.62 |
0.60 | 0.71 | 0.53 |
0.70 | 0.81 | 0.44 |
0.80 | 0.84 | 0.32 |
0.90 | 0.88 | 0.21 |
1.00 | 1.00 | 0.02 |
Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.) |