NucPred on Proteomes

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):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR 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:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

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
Q09437 UniProt NPD GO	YP62_CAEEL	Putative serine/threonine-protein kinase B0495.2 (EC 2.7.11.1)	0.98	-	nuc	0					719
Q2TJ95 UniProt NPD GO	RSPO3_MOUSE	R-spondin-3 precursor (Roof plate-specific spondin-3) (Cysteine-rich and single thrombospondin domai ...	0.98	+	nuc	0	Secreted protein				277
Q18919 UniProt NPD GO	RCOR_CAEEL	REST corepressor spr-1 (CoREST) (Suppressor of presenilin 1)	0.98	-	nuc	0	Nucleus				558
P51862 UniProt NPD GO	ROM2_YEAST	RHO1 GDP-GTP exchange protein 2	0.98	-	nuc	0		bud tip [IDA]			1356
Q8IYW5 UniProt NPD GO	RN168_HUMAN	RING finger protein 168	0.98	+	nuc	0					571
Q80XJ2 UniProt NPD GO	RN168_MOUSE	RING finger protein 168	0.98	-	nuc	0					550
P52756 UniProt NPD GO	RBM5_HUMAN	RNA-binding protein 5 (RNA-binding motif protein 5) (Putative tumor suppressor LUCA15) (G15 protein) ...	0.98	+	nuc	0	Nucleus (Potential)	nucleus [TAS]	606884		815
Q13905 UniProt NPD GO	RPGF1_HUMAN	Rap guanine nucleotide exchange factor 1 (Guanine nucleotide-releasing factor 2) (C3G protein) (CRK ...	0.98	-	nuc	0			600303		1077
Q8CHG7 UniProt NPD GO	RPGF2_MOUSE	Rap guanine nucleotide exchange factor 2 (Neural RAP guanine nucleotide exchange protein) (nRap GEP) ...	0.98	-	nuc	0	Cell membrane (By similarity). Associated with the synaptic plasma membrane (By similarity)	integral to plasma membrane [ISS] membrane [ISS]			1138
Q9Y4G8 UniProt NPD GO	RPGF2_HUMAN	Rap guanine nucleotide exchange factor 2 (Neural RAP guanine nucleotide exchange protein) (nRap GEP) ...	0.98	-	nuc	0	Cell membrane (By similarity). Associated with the synaptic plasma membrane (By similarity)	integral to plasma membrane [NAS] membrane [IDA]	609530		1499
Q96PV0 UniProt NPD GO	SYGP1_HUMAN	Ras GTPase-activating protein SynGAP (Synaptic Ras-GTPase-activating protein 1) (Synaptic Ras-GAP 1) ...	0.98	+	nuc	0			603384		1328
Q9QUH6 UniProt NPD GO	SYGP1_RAT	Ras GTPase-activating protein SynGAP (Synaptic Ras-GTPase-activating protein 1) (Synaptic Ras-GAP 1) ...	0.98	+	nuc	0	Membrane; peripheral membrane protein. Mostly in excitatory glutamatergic synapses				1293
Q9EQZ7 UniProt NPD GO	RIMS2_MOUSE	Regulating synaptic membrane exocytosis protein 2 (Rab3-interacting molecule 2) (RIM 2) (Rab3-intera ...	0.98	+	nuc	0					1530
P49797 UniProt NPD GO	RGS3_RAT	Regulator of G-protein signaling 3 (RGS3) (SRB-RGS)	0.98	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Nucleus (By simila ...				967
Q9BZI7 UniProt NPD GO	REN3B_HUMAN	Regulator of nonsense transcripts 3B (Nonsense mRNA reducing factor 3B) (Up-frameshift suppressor 3 ...	0.98	+	nuc	0	Nucleus. Cytoplasm. Shuttling between the nucleus and the cytoplasm	cytoplasm [NAS] nucleus [NAS]		1UW4	483
Q757K3 UniProt NPD GO	MAF1_ASHGO	Repressor of RNA polymerase III transcription MAF1	0.98	+	nuc	0	Nucleus (By similarity)				397
Q96T21 UniProt NPD GO	SEBP2_HUMAN	SECIS-binding protein 2 (Selenocysteine insertion sequence-binding protein 2)	0.98	+	nuc	0	Nucleus (Potential)		609698		854
Q9Z180 UniProt NPD GO	SETBP_MOUSE	SET-binding protein (SEB)	0.98	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			1535
P43612 UniProt NPD GO	SA155_YEAST	SIT4-associating protein SAP155	0.98	+	nuc	0	Cytoplasm	cytoplasm [IPI]			1002
O08815 UniProt NPD GO	SLK_RAT	STE20-like serine/threonine-protein kinase (EC 2.7.11.1) (STE20-like kinase) (STE20-related serine/t ...	0.98	-	nuc	0	Cytoplasm (By similarity)				1206
Q04692 UniProt NPD GO	SMRCD_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD ...	0.98	+	nuc	0	Nucleus	nuclear matrix [ISS] nucleus [IDA]			1021
Q752S6 UniProt NPD GO	SWC4_ASHGO	SWR1-complex protein 4	0.98	+	nuc	0	Nucleus (By similarity)				488
Q6FTV1 UniProt NPD GO	SWC4_CANGA	SWR1-complex protein 4	0.98	+	nuc	0	Nucleus (By similarity)				532
Q4HY90 UniProt NPD GO	SWC4_GIBZE	SWR1-complex protein 4	0.98	-	nuc	0	Nucleus (By similarity)				570
P16014 UniProt NPD GO	SCG1_MOUSE	Secretogranin-1 precursor (Secretogranin I) (SgI) (Chromogranin B) (CgB)	0.98	-	exc	0	Neuroendocrine and endocrine secretory granules				677
Q9P0U3 UniProt NPD GO	SENP1_HUMAN	Sentrin-specific protease 1 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP1)	0.98	+	nuc	0	Nucleus	nucleus [TAS]		2CKH	643
Q13315 UniProt NPD GO	ATM_HUMAN	Serine-protein kinase ATM (EC 2.7.11.1) (Ataxia telangiectasia mutated) (A-T, mutated)	0.98	-	end	0	Nucleus. Cytoplasmic vesicle. Primarily nuclear. Found also in endocytic vesicles in association wit ...		607585		3056
P15442 UniProt NPD GO	GCN2_YEAST	Serine/threonine-protein kinase GCN2 (EC 2.7.11.1)	0.98	-	nuc	0	Ribosome. Associates with the 60S subunit of ribosomes	cytosolic ribosome (sensu Eukaryota) [IDA]		1ZYD	1590
O54874 UniProt NPD GO	MRCKA_RAT	Serine/threonine-protein kinase MRCK alpha (EC 2.7.11.1) (CDC42-binding protein kinase alpha) (Myoto ...	0.98	+	nuc	0	Cytoplasm. Displays a dispersed punctate distribution and concentrates along the cell periphery, esp ...	intercellular junction [IDA] leading edge [IDA]			1732
P51954 UniProt NPD GO	NEK1_MOUSE	Serine/threonine-protein kinase Nek1 (EC 2.7.11.1) (NimA-related protein kinase 1)	0.98	+	nuc	0	Nucleus (Probable)				1203
Q13523 UniProt NPD GO	PRP4B_HUMAN	Serine/threonine-protein kinase PRP4 homolog (EC 2.7.11.1) (PRP4 pre-mRNA-processing factor 4 homolo ...	0.98	+	nuc	0	Nucleus		602338		1007
Q96WV9 UniProt NPD GO	CDK9_SCHPO	Serine/threonine-protein kinase cdk9 (EC 2.7.11.1) (Cyclin-dependent kinase cdk9)	0.98	-	nuc	0	Nucleus	nucleus [IDA]			591
P34314 UniProt NPD GO	TLK1_CAEEL	Serine/threonine-protein kinase tousled-like 1 (EC 2.7.11.1) (Tousled-like kinase 1)	0.98	-	nuc	0	Nucleus	nucleus [IDA]			965
O55047 UniProt NPD GO	TLK2_MOUSE	Serine/threonine-protein kinase tousled-like 2 (EC 2.7.11.1) (Tousled-like kinase 2)	0.98	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			718
Q4KLP8 UniProt NPD GO	SGOL1_XENLA	Shugoshin-like 1 (Xsgo)	0.98	+	nuc	0	Nucleus. Localizes to the centromere. At anaphase, it dissociates from centromeres when chromatids s ...				663
Q5FBB7 UniProt NPD GO	SGOL1_HUMAN	Shugoshin-like 1 (hSgo1) (Serologically defined breast cancer antigen NY-BR-85)	0.98	+	nuc	0	Nucleus. Localizes to the centromere. BUB1 is required for centromeric localization. During prometap ...		609168		561
Q07889 UniProt NPD GO	SOS1_HUMAN	Son of sevenless homolog 1 (SOS-1)	0.98	-	nuc	0			135300	1XDV	1333
Q07890 UniProt NPD GO	SOS2_HUMAN	Son of sevenless homolog 2 (SOS-2)	0.98	+	nuc	0			601247		1332
P34402 UniProt NPD GO	SAS4_CAEEL	Spindle assembly abnormal protein 4	0.98	-	nuc	0	Centrosome. Localizes to the centrosome throughout the cell cycle. Localizes to a tiny dot in the ce ...				808
Q8BZX4 UniProt NPD GO	SFR12_MOUSE	Splicing factor, arginine/serine-rich 12 (Serine-arginine-rich-splicing regulatory protein 86) (SRrp ...	0.98	+	nuc	0	Nucleus (By similarity)				494
Q9JKL7 UniProt NPD GO	SFR12_RAT	Splicing factor, arginine/serine-rich 12 (Serine-arginine-rich-splicing regulatory protein 86) (SRrp ...	0.98	+	nuc	0	Nucleus				494
Q8WXA9 UniProt NPD GO	SFR12_HUMAN	Splicing factor, arginine/serine-rich 12 (Serine-arginine-rich-splicing regulatory protein 86) (SRrp ...	0.98	+	nuc	0	Nucleus				508
Q696W0 UniProt NPD GO	SPEG_BRARE	Striated muscle preferentially expressed protein kinase (EC 2.7.11.1)	0.98	+	nuc	0	Nucleus (By similarity)	Z disc [NAS]			2995
Q12267 UniProt NPD GO	SMC4_YEAST	Structural maintenance of chromosome 4	0.98	+	nuc	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	nuclear condensin complex [IPI]			1418
Q8K4L3 UniProt NPD GO	SVIL_MOUSE	Supervillin (Archvillin) (p205/p250)	0.98	+	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoskeleton. Tightly associated with ...				2170
Q93148 UniProt NPD GO	SPT6H_CAEBR	Suppressor of Ty 6 homolog (Abnormal embryogenesis protein 5)	0.98	+	nuc	0	Nucleus (Probable)				1521
P34703 UniProt NPD GO	SPT6H_CAEEL	Suppressor of Ty 6 homolog (Abnormal embryogenesis protein 5)	0.98	+	nuc	0	Nucleus (Probable)				1521
O70608 UniProt NPD GO	SYCP2_RAT	Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein) (rnSCP2)	0.98	+	nuc	0	Nucleus. In axial/lateral elements of the tripartite segments of synaptonemal complexes	nucleus [ISS] synaptonemal complex [ISS]			1505
Q99N50 UniProt NPD GO	SYTL2_MOUSE	Synaptotagmin-like protein 2 (Exophilin-4)	0.98	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Bound to melanosomes. Isoform 1 is localized ...	extrinsic to plasma membrane [IDA] melanosome [IDA] membrane fraction [IDA]			950
Q60610 UniProt NPD GO	TIAM1_MOUSE	T-lymphoma invasion and metastasis-inducing protein 1 (TIAM-1 protein)	0.98	-	nuc	0		plasma membrane [IDA]		1FOE	1591

You are viewing entries 801 to 850 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.