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

NucPred - predictions for eukaryotic proteomes

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)    
You can bookmark/save your search criteria with this link. You can also start again with default settings.
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
P38854
UniProt
NPD  GO
YHV9_YEAST Uncharacterized protein YHR159W 0.93 - nuc 0 cytoplasm [IDA] 504
P38870
UniProt
NPD  GO
YHY2_YEAST Uncharacterized protein YHR182W 0.93 - nuc 0 cytoplasm [IDA] 785
P40498
UniProt
NPD  GO
YIJ1_YEAST Uncharacterized protein YIL091C 0.93 - nuc 0 nucleolus [IDA]
nucleus [IDA]
721
Q99299
UniProt
NPD  GO
YP158_YEAST Uncharacterized protein YPL158C 0.93 + nuc 0 bud neck [IDA] 758
Q03944
UniProt
NPD  GO
VPS64_YEAST Vacuolar protein sorting protein 64 (Factor arrest protein 9) 0.93 - nuc 0 Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (Potenti ... cytoplasm [IDA]
endoplasmic reticulum membrane [IDA]
604
P16612
UniProt
NPD  GO
VEGFA_RAT Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF) 0.93 + nuc 0 Secreted protein (By similarity). VEGF-A120 is acidic and freely secreted. VEGF-A164 is more basic, ... 214
Q8C761
UniProt
NPD  GO
WDR60_MOUSE WD repeat protein 60 0.93 + nuc 0 999
P48234
UniProt
NPD  GO
YG3J_YEAST WD repeat protein YGR145W 0.93 + nuc 0 nucleolus [IDA] 707
Q03177
UniProt
NPD  GO
YMZ2_YEAST WD repeat protein YMR102C 0.93 + nuc 0 834
P46941
UniProt
NPD  GO
YLE5_CAEEL WW domain-containing protein C38D4.5 0.93 - nuc 0 837
O09053
UniProt
NPD  GO
WRN_MOUSE Werner syndrome ATP-dependent helicase homolog (EC 3.6.1.-) 0.93 - nuc 0 Nucleus 1401
Q99MZ3
UniProt
NPD  GO
WBS14_MOUSE Williams-Beuren syndrome chromosome region 14 protein homolog (Mlx interactor) (MLX-interacting prot ... 0.93 - nuc 0 Nucleus (By similarity) transcription factor complex [IDA] 864
Q8VHI6
UniProt
NPD  GO
WASF3_MOUSE Wiskott-Aldrich syndrome protein family member 3 (WASP-family protein member 3) (Protein WAVE-3) 0.93 + nuc 0 Cytoplasm (By similarity) 501
P25992
UniProt
NPD  GO
YEMA_DROME Yemanuclein-alpha 0.93 + nuc 0 Nucleus nucleus [TAS] 1002
Q66IH9
UniProt
NPD  GO
ZCHC4_XENTR Zinc finger CCHC domain-containing protein 4 0.93 + nuc 0 487
Q8NAP3
UniProt
NPD  GO
ZBT38_HUMAN Zinc finger and BTB domain-containing protein 38 0.93 - nuc 0 Nucleus (By similarity) nucleus [ISS] 1195
Q4R361
UniProt
NPD  GO
ZN645_MACFA Zinc finger protein 645 0.93 - nuc 0 422
Q9BU19
UniProt
NPD  GO
ZN692_HUMAN Zinc finger protein 692 0.93 + nuc 0 Nucleus (Probable) 519
Q3U381
UniProt
NPD  GO
ZN692_MOUSE Zinc finger protein 692 0.93 + nuc 0 Nucleus (Probable) 531
P55879
UniProt
NPD  GO
GLI3_CHICK Zinc finger protein GLI3 (Fragment) 0.93 - nuc 0 Nucleus 663
Q91661
UniProt
NPD  GO
GLI4_XENLA Zinc finger protein GLI4 (Neural-specific DNA-binding protein xGLI4) (xGLI-4) 0.93 - nuc 0 Nucleus (Potential) 1361
O35615
UniProt
NPD  GO
FOG1_MOUSE Zinc finger protein ZFPM1 (Zinc finger protein multitype 1) (Friend of GATA protein 1) (Friend of GA ... 0.93 - nuc 0 Nucleus nucleus [IDA] 1SRK 995
P51984
UniProt
NPD  GO
CREB_CHLVR cAMP response element-binding protein 0.93 + nuc 0 Nucleus 249
Q5AM44
UniProt
NPD  GO
RNA14_CANAL mRNA 3'-end processing protein RNA14 0.93 - nuc 0 Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity) 791
Q5KU05
UniProt
NPD  GO
PALA_ASPOR pH-response regulator protein palA/RIM20 0.93 - nuc 0 828
Q873Y3
UniProt
NPD  GO
PACC_CANDU pH-response transcription factor pacC/RIM101 0.93 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity) 666
Q870A3
UniProt
NPD  GO
PACC_FUSOX pH-response transcription factor pacC/RIM101 0.93 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity) 609
Q9UW14
UniProt
NPD  GO
PACC_CANAL pH-response transcription factor pacC/RIM101 (pH-response regulator protein 2) 0.93 - nuc 0 Cytoplasm (By similarity). Nucleus (By similarity) 661
Q96NA8
UniProt
NPD  GO
TSNA1_HUMAN t-SNARE domain-containing protein 1 0.93 - nuc 1 513
Q2T9V5
UniProt
NPD  GO
TRM6_BOVIN tRNA (adenine-N(1)-)-methyltransferase non-catalytic subunit TRM6 (tRNA(m1A58)-methyltransferase sub ... 0.93 + nuc 0 Nucleus (By similarity) 497
Q8IZH2
UniProt
NPD  GO
XRN1_HUMAN 5'-3' exoribonuclease 1 (EC 3.1.11.-) (Strand-exchange protein 1 homolog) 0.92 - nuc 0 Cytoplasm. Discrete foci at the inner surface of the cell membrane 607994 1706
Q62924
UniProt
NPD  GO
AKA11_RAT A-kinase anchor protein 11 (Protein kinase A-anchoring protein 11) (PRKA11) (A-kinase anchor protein ... 0.92 + nuc 0 Peroxisome peroxisome [IDA] 1129
O43823
UniProt
NPD  GO
AKAP8_HUMAN A-kinase anchor protein 8 (A-kinase anchor protein 95 kDa) (AKAP 95) 0.92 + nuc 0 Nucleus; nucleoplasm; nuclear matrix. Associated with the nuclear matrix. Redistributed and detached ... nucleus [TAS] 604692 692
Q9R0L7
UniProt
NPD  GO
AKP8L_MOUSE A-kinase anchor protein 8-like (AKAP8-like protein) (Neighbor of A-kinase-anchoring protein 95) (Nei ... 0.92 + nuc 0 Nucleus; nucleoplasm; nuclear matrix (By similarity). Cytoplasm (By similarity). Nuclear at steady s ... 642
P14196
UniProt
NPD  GO
AAC2_DICDI AAC-rich mRNA clone AAC11 protein (Fragment) 0.92 + nuc 0 448
Q9Y2X7
UniProt
NPD  GO
GIT1_HUMAN ARF GTPase-activating protein GIT1 (G protein-coupled receptor kinase-interactor 1) (GRK-interacting ... 0.92 - nuc 0 Cytoplasm. Cycles between at least 3 distinct intracellular compartments, including focal adhesions, ... 608434 761
Q8BM75
UniProt
NPD  GO
ARI5B_MOUSE AT-rich interactive domain-containing protein 5B (ARID domain-containing protein 5B) (MRF1-like) (Mo ... 0.92 - nuc 0 Nucleus 1188
Q6FNA2
UniProt
NPD  GO
DBP10_CANGA ATP-dependent RNA helicase DBP10 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 969
Q6CIR0
UniProt
NPD  GO
DBP10_KLULA ATP-dependent RNA helicase DBP10 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 973
Q6BXG0
UniProt
NPD  GO
DBP4_DEBHA ATP-dependent RNA helicase DBP4 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 766
Q8K4L0
UniProt
NPD  GO
DDX54_MOUSE ATP-dependent RNA helicase DDX54 (EC 3.6.1.-) (DEAD box protein 54) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) nucleolus [ISS]
nucleus [ISS]
874
P38112
UniProt
NPD  GO
MAK5_YEAST ATP-dependent RNA helicase MAK5 (EC 3.6.1.-) (Maintenance of killer protein 5) 0.92 - nuc 0 Nucleus; nucleolus nucleolus [IDA] 773
Q2UHC1
UniProt
NPD  GO
DBP10_ASPOR ATP-dependent RNA helicase dbp10 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 929
Q2UE66
UniProt
NPD  GO
DBP7_ASPOR ATP-dependent RNA helicase dbp7 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 760
O60173
UniProt
NPD  GO
DBP7_SCHPO ATP-dependent RNA helicase dbp7 (EC 3.6.1.-) 0.92 - nuc 0 Nucleus; nucleolus (By similarity) 709
Q4WRH5
UniProt
NPD  GO
ROK1_ASPFU ATP-dependent RNA helicase rok1 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 739
Q2UQW3
UniProt
NPD  GO
ROK1_ASPOR ATP-dependent RNA helicase rok1 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 725
Q5BET6
UniProt
NPD  GO
ROK1_EMENI ATP-dependent RNA helicase rok1 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 742
Q59N29
UniProt
NPD  GO
SPB41_CANAL ATP-dependent rRNA helicase SPB41 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 631
Q59NP8
UniProt
NPD  GO
SPB42_CANAL ATP-dependent rRNA helicase SPB42 (EC 3.6.1.-) 0.92 + nuc 0 Nucleus; nucleolus (By similarity) 631

You are viewing entries 3101 to 3150 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.