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
P13361 UniProt NPD GO	HUNB_DROVI	Protein hunchback	0.83	-	nuc	0	Nucleus (By similarity)				816
Q6AZ28 UniProt NPD GO	PIAS2_RAT	Protein inhibitor of activated STAT2 (Protein inhibitor of activated STAT x) (Msx-interacting-zinc f ...	0.83	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes at least partially with promyelocytic leukemia nu ...				572
P18490 UniProt NPD GO	PCX_DROME	Protein pecanex	0.83	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				3433
O15297 UniProt NPD GO	PP2CD_HUMAN	Protein phosphatase 2C isoform delta (EC 3.1.3.16) (PP2C-delta) (p53-induced protein phosphatase 1) ...	0.83	-	nuc	0		nucleus [TAS]	605100		605
Q76I76 UniProt NPD GO	SSH2_HUMAN	Protein phosphatase Slingshot homolog 2 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-2L) (hSSH-2L)	0.83	-	nuc	0			606779		1423
O74653 UniProt NPD GO	POB1_SCHPO	Protein pob1 (BOI protein homolog)	0.83	-	exc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated at the cell tips during interp ...	cell cortex of cell tip [IDA]			871
P91682 UniProt NPD GO	SMO_DROME	Protein smoothened precursor (dSMO) (SMOH) (Smooth)	0.83	-	end	6 *	Membrane; multi-pass membrane protein	endosome [TAS] integral to membrane [TAS] plasma membrane [TAS]			1036
P17789 UniProt NPD GO	TTKB_DROME	Protein tramtrack, beta isoform (Tramtrack p69) (Repressor protein fushi tarazu)	0.83	-	nuc	0	Nucleus	polytene chromosome [IDA]		2DRP	643
P30619 UniProt NPD GO	SEC1_YEAST	Protein transport protein SEC1	0.83	+	nuc	0		bud neck [IDA] bud tip [IDA] plasma membrane [IDA]			724
Q85B60 UniProt NPD GO	YCF2_ADICA	Protein ycf2	0.83	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2104
Q58EX7 UniProt NPD GO	PKHG4_HUMAN	Puratrophin-1 (Pleckstrin homology domain-containing family G member 4) (Purkinje cell atrophy-assoc ...	0.83	-	nuc	0			609526		1191
Q9FF61 UniProt NPD GO	SM3L1_ARATH	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member ...	0.83	+	mit	0	Nucleus (By similarity)				881
Q23622 UniProt NPD GO	TBX36_CAEEL	Putative T-box protein 36	0.83	-	nuc	0	Nucleus (Potential)				331
O15818 UniProt NPD GO	IF3X_DICDI	Putative eukaryotic translation initiation factor 3 subunit (eIF-3)	0.83	-	nuc	0					1321
Q20085 UniProt NPD GO	YPS7_CAEEL	Putative serine/threonine-protein kinase F35H8.7 (EC 2.7.11.1)	0.83	-	nuc	0					468
Q10144 UniProt NPD GO	YAS8_SCHPO	Putative transcriptional regulatory protein C3H8.08c	0.83	+	nuc	0	Nucleus (Probable)				563
Q9C9F6 UniProt NPD GO	APRR6_ARATH	Putative two-component response regulator-like APRR6 (Pseudo-response regulator 6)	0.83	-	nuc	0	Nucleus (Probable)				663
P42083 UniProt NPD GO	YKCA_CAEEL	Putative tyrosine-protein phosphatase B0280.11 (EC 3.1.3.48)	0.83	+	nuc	0					441
Q7Z142 UniProt NPD GO	YO15_CAEEL	Putative zinc finger protein ZK686.5	0.83	+	nuc	0	Nucleus (Probable)				202
O15553 UniProt NPD GO	MEFV_HUMAN	Pyrin (Marenostrin)	0.83	-	nuc	0	Isoform 1: Cytoplasm. Associated with microtubules and with the filamentous actin of perinuclear fil ...	microtubule associated complex [IDA] nucleus [IDA]	608107		781
Q9QZS2 UniProt NPD GO	RNF4_MOUSE	RING finger protein 4	0.83	-	mit	0	Cytoplasm. Nucleus				194
Q6FP41 UniProt NPD GO	TFB2_CANGA	RNA polymerase II transcription factor B subunit 2 (RNA polymerase II transcription factor B p52 sub ...	0.83	-	mit	0	Nucleus (By similarity)				504
Q80XA6 UniProt NPD GO	REPS2_MOUSE	RalBP1-associated Eps domain-containing protein 2 (RalBP1-interacting protein 2) (Partner of RalBP1) ...	0.83	-	nuc	0	Cytoplasm (By similarity)				521
P13784 UniProt NPD GO	FLP_ZYGBI	Recombinase Flp protein	0.83	+	nuc	0					568
O46470 UniProt NPD GO	RGS7_BOVIN	Regulator of G-protein signaling 7 (RGS7)	0.83	-	nuc	0					469
P25042 UniProt NPD GO	ROX1_YEAST	Repressor ROX1 (Hypoxic function repressor) (Heme-dependent repression factor)	0.83	+	nuc	0	Nucleus	nuclear chromosome [IPI]			368
Q5FBR4 UniProt NPD GO	RARA_CANFA	Retinoic acid receptor alpha (RAR-alpha)	0.83	+	nuc	0	Nucleus (By similarity)				462
Q7TNR9 UniProt NPD GO	ARHG4_MOUSE	Rho guanine nucleotide exchange factor 4 (APC-stimulated guanine nucleotide exchange factor) (Asef)	0.83	+	nuc	0	Cytoplasm. Colocalized with APC in the synapse of olfactory glomerulus				484
P70335 UniProt NPD GO	ROCK1_MOUSE	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.83	-	nuc	0	Cytoplasm. Associated with the mother centriole and an intercentriolar linker. Golgi apparatus; Golg ...				1354
Q60875 UniProt NPD GO	ARHG2_MOUSE	Rho/Rac guanine nucleotide exchange factor 2 (Lymphoid blast crisis-like 1) (LBC'S first cousin) (On ...	0.83	-	nuc	0	Cytoplasm (By similarity). Colocalizes with microtubules through the C-terminal coiled-coil domain ( ...	cell soma [IDA] dendritic shaft [IDA]			596
Q06412 UniProt NPD GO	TUS1_YEAST	Rho1 guanine nucleotide exchange factor TUS1 (TOR unique function suppressor protein 1)	0.83	-	nuc	0					1307
Q5F3L1 UniProt NPD GO	KS6A5_CHICK	Ribosomal protein S6 kinase alpha-5 (EC 2.7.11.1)	0.83	+	cyt	0	Nucleus (By similarity)				789
Q5QT59 UniProt NPD GO	RSA3_PICAN	Ribosome assembly protein 3	0.83	-	nuc	0	Nucleus; nucleolus (By similarity)				152
Q9Y6N7 UniProt NPD GO	ROBO1_HUMAN	Roundabout homolog 1 precursor (H-Robo-1) (Deleted in U twenty twenty)	0.83	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)	cell surface [IDA] integral to plasma membrane [TAS]	602430		1651
Q9WV48 UniProt NPD GO	SHAN1_RAT	SH3 and multiple ankyrin repeat domains protein 1 (Shank1) (GKAP/SAPAP-interacting protein) (SPANK-1 ...	0.83	-	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. Colocalizes with alpha-latrotoxin receptor 1	postsynaptic membrane [IDA]		1Q3P	2167
Q9TTA5 UniProt NPD GO	SMAL1_BOVIN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 ...	0.83	-	nuc	0	Nucleus (By similarity)				941
Q8BH34 UniProt NPD GO	SEM3D_MOUSE	Semaphorin-3D precursor	0.83	+	nuc	1 *	Secreted protein (By similarity)				777
Q95196 UniProt NPD GO	SEMG2_MACMU	Semenogelin-2 precursor (Semenogelin II) (SGII)	0.83	-	nuc	0	Secreted protein				706
O54748 UniProt NPD GO	STK3_RAT	Serine/threonine-protein kinase 3 (EC 2.7.11.1) (STE20-like kinase MST2) (MST-2) (Mammalian STE20-li ...	0.83	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)				491
Q62101 UniProt NPD GO	KPCD1_MOUSE	Serine/threonine-protein kinase D1 (EC 2.7.11.13) (nPKC-D1) (Protein kinase D) (Protein kinase C mu ...	0.83	-	nuc	0					918
Q8K1Y2 UniProt NPD GO	KPCD3_MOUSE	Serine/threonine-protein kinase D3 (EC 2.7.11.13) (Protein kinase C nu type) (nPKC-nu)	0.83	-	mit	0					889
O95835 UniProt NPD GO	LATS1_HUMAN	Serine/threonine-protein kinase LATS1 (EC 2.7.11.1) (Large tumor suppressor homolog 1) (WARTS protei ...	0.83	-	nuc	0	Centrosome. Localizes to the centrosomes throughout interphase but migrates to the mitotic apparatus ...	spindle pole [IDA]	603473		1130
Q80UW5 UniProt NPD GO	MRCKG_MOUSE	Serine/threonine-protein kinase MRCK gamma (EC 2.7.11.1) (CDC42-binding protein kinase gamma) (Myoto ...	0.83	-	nuc	0	Cytoplasm. Concentrates at the leading edge of cells (By similarity)	leading edge [ISS]			1551
P51956 UniProt NPD GO	NEK3_HUMAN	Serine/threonine-protein kinase Nek3 (EC 2.7.11.1) (NimA-related protein kinase 3) (HSPK 36)	0.83	-	nuc	0		nucleus [NAS]	604044		506
P70032 UniProt NPD GO	PLK1_XENLA	Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-1) (Plx1)	0.83	-	nuc	0	Nucleus. Centrosome. Localized at centrosomes at prophase, spindles at metaphase, and at the midbody ...				598
P53351 UniProt NPD GO	PLK2_MOUSE	Serine/threonine-protein kinase PLK2 (EC 2.7.11.21) (Polo-like kinase 1) (PLK-2) (Serine/threonine-p ...	0.83	-	nuc	0					682
Q6CVA2 UniProt NPD GO	STE20_KLULA	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.83	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				989
Q6CAD2 UniProt NPD GO	ATM_YARLI	Serine/threonine-protein kinase TEL1 (EC 2.7.11.1) (DNA-damage checkpoint kinase TEL1) (Telomere len ...	0.83	-	end	0	Nucleus. Localizes to nuclear DNA repair foci with other DNA repair proteins in response to DNA doub ...				2282
O14019 UniProt NPD GO	HAL4_SCHPO	Serine/threonine-protein kinase hal4 (EC 2.7.11.1) (Halotolerence protein 4)	0.83	-	nuc	0					636
Q61CW2 UniProt NPD GO	SMG1_CAEBR	Serine/threonine-protein kinase smg-1 (EC 2.7.11.1) (Suppressor with morphogenetic effect on genital ...	0.83	-	cyt	2	Cytoplasm (By similarity)				2319

You are viewing entries 7551 to 7600 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.