SBC logo Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

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).

Species:  

Note: All filters/tests are combined with AND unless otherwise stated
Show only the proteins with links to database(s):


( combination )
Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)
UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the
Only show proteins where the PredictNLS prediction is:

Only show proteins where the PSORT II predicted location
Click here: to filter by NucPred score  
exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)
export all ACs and IDs as text file
Show proteins (ordered by NucPred score ) from to   (currently 98716 matches)    
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: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

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.)

Go back to the NucPred Home Page.