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
Q9LVD8 UniProt NPD GO	CAP7_ARATH	Putative clathrin assembly protein At5g57200	0.64	-	nuc	0					591
Q9SJA4 UniProt NPD GO	CNG14_ARATH	Putative cyclic nucleotide-gated ion channel 14 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.64	+	end	6	Cell membrane; multi-pass membrane protein (Potential)				726
Q6L406 UniProt NPD GO	R1B19_SOLDE	Putative late blight resistance protein homolog R1B-19	0.64	+	end	0	Cytoplasm (By similarity)				1582
P25627 UniProt NPD GO	BUD23_YEAST	Putative methyltransferase BUD23 (EC 2.1.1.-) (Bud site selection protein 23)	0.64	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			275
Q7PC81 UniProt NPD GO	PDR15_ARATH	Putative pleiotropic drug resistance protein 15	0.64	-	end	11	Membrane; multi-pass membrane protein (By similarity)				1390
Q67ER4 UniProt NPD GO	R113A_BOVIN	RING finger protein 113A (Zinc finger protein 183)	0.64	+	nuc	0					343
O94646 UniProt NPD GO	MED8_SCHPO	RNA polymerase II mediator complex subunit 8 (Cell separation protein sep15) (RNA polymerase II tran ...	0.64	-	nuc	0	Nucleus (Potential)	mediator complex [IDA]			200
Q61545 UniProt NPD GO	EWS_MOUSE	RNA-binding protein EWS	0.64	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Cell surface (By similarity). Relocates from cyt ...	nucleus [IDA]			655
Q01844 UniProt NPD GO	EWS_HUMAN	RNA-binding protein EWS (EWS oncogene) (Ewing sarcoma breakpoint region 1 protein)	0.64	+	nuc	0	Nucleus. Cytoplasm. Cell surface. Relocates from cytoplasm to ribosomes upon PTK2B/FAK2 activation		133450	2CPE	656
O59784 UniProt NPD GO	MDE7_SCHPO	RNA-binding protein mde7 (Mei4-dependent protein 7)	0.64	-	nuc	0					761
Q5ND29 UniProt NPD GO	RILP_MOUSE	Rab-interacting lysosomal protein	0.64	-	nuc	0	Intracytoplasmic membrane (By similarity). Endosome; late endosome; late endosomal membrane (By simi ...				369
Q4ZG46 UniProt NPD GO	RBP24_HUMAN	Ran-binding protein 2-like 4 (RanBP2L4)	0.64	-	nuc	0					1583
Q5R4Y2 UniProt NPD GO	RANB3_PONPY	Ran-binding protein 3 (RanBP3)	0.64	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				494
Q8WQ53 UniProt NPD GO	RAB21_GEOCY	Ras-related protein Rab-21	0.64	-	nuc	0	Golgi apparatus; Golgi membrane; lipid-anchor (By similarity)				229
P13783 UniProt NPD GO	FLP_KLULA	Recombinase Flp protein	0.64	-	nuc	0					447
O95980 UniProt NPD GO	RECK_HUMAN	Reversion-inducing cysteine-rich protein with Kazal motifs precursor (hRECK) (Suppressor of tumorige ...	0.64	+	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	membrane fraction [TAS]	605227		971
Q8C033 UniProt NPD GO	ARHGA_MOUSE	Rho guanine nucleotide exchange factor 10	0.64	-	end	0					1345
O74335 UniProt NPD GO	RGA5_SCHPO	Rho-GTPase-activating protein 5	0.64	-	nuc	0	Membrane-associated. Localizes to the cell poles and septum	cell tip [IDA] medial ring [IDA]			361
P15467 UniProt NPD GO	RNAS4_BOVIN	Ribonuclease 4 (EC 3.1.27.-) (RNase 4) (Ribonuclease BL4)	0.64	-	nuc	0	Secreted protein				119
Q02933 UniProt NPD GO	RNY1_YEAST	Ribonuclease T2-like precursor (EC 3.1.27.1) (RNase T2-like)	0.64	-	exc	0	Secreted protein	extracellular region [IDA]			434
Q08235 UniProt NPD GO	BRX1_YEAST	Ribosome biogenesis protein BRX1	0.64	-	nuc	0	Nucleus; nucleolus	nucleolus [IPI]			291
Q759D1 UniProt NPD GO	RLP24_ASHGO	Ribosome biogenesis protein RLP24	0.64	-	nuc	0	Nucleus; nucleolus (By similarity)				197
O74994 UniProt NPD GO	RNG3_SCHPO	Ring assembly protein 3	0.64	-	mit	0	Cytoplasm. Associated with the actinomyosin ring	actin cytoskeleton [TAS]			746
Q13950 UniProt NPD GO	RUNX2_HUMAN	Runt-related transcription factor 2 (Core-binding factor, alpha 1 subunit) (CBF-alpha 1) (Acute myel ...	0.64	-	nuc	0	Nucleus		600211		521
Q08775 UniProt NPD GO	RUNX2_MOUSE	Runt-related transcription factor 2 (Core-binding factor, alpha 1 subunit) (CBF-alpha 1) (Acute myel ...	0.64	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			607
Q9ERC3 UniProt NPD GO	SRTD3_MOUSE	SERTA domain-containing protein 3 (Replication protein-binding trans-activator) (RPA-binding trans-a ...	0.64	-	nuc	0	Nucleus (By similarity)				197
Q96PX8 UniProt NPD GO	SLIK1_HUMAN	SLIT and NTRK-like protein 1 precursor (Leucine-rich repeat-containing protein 12)	0.64	-	end	1	Membrane; single-pass membrane protein (Potential)		609678		696
O74536 UniProt NPD GO	SNF1_SCHPO	SNF1-like protein kinase ssp2 (EC 2.7.11.1)	0.64	-	cyt	0					576
Q9BXA9 UniProt NPD GO	SALL3_HUMAN	Sal-like protein 3 (Zinc finger protein SALL3) (hSALL3)	0.64	-	nuc	0	Nucleus (Probable)		605079		1300
Q03517 UniProt NPD GO	SCG2_MOUSE	Secretogranin-2 precursor (Secretogranin II) (SgII) (Chromogranin C) [Contains: Secretoneurin (SN)]	0.64	-	exc	1 *	Neuroendocrine and endocrine secretory granules	extracellular space [ISS]			617
Q9WTM3 UniProt NPD GO	SEM6C_MOUSE	Semaphorin-6C precursor (Semaphorin Y) (Sema Y)	0.64	-	exc	1	Membrane; single-pass type I membrane protein				931
Q5R7F5 UniProt NPD GO	SEM6D_PONPY	Semaphorin-6D precursor	0.64	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1017
Q5R481 UniProt NPD GO	SEPT7_PONPY	Septin-7	0.64	-	nuc	0					437
Q9Z265 UniProt NPD GO	CHK2_MOUSE	Serine/threonine-protein kinase Chk2 (EC 2.7.11.1)	0.64	-	nuc	0	Nucleus				546
Q91819 UniProt NPD GO	STK6L_XENLA	Serine/threonine-protein kinase Eg2-like (EC 2.7.11.1) (p46XlEg22)	0.64	-	nuc	0	Spindle (By similarity). Centrosome (By similarity). Localizes to the spindle pole during mitosis es ...				408
Q16513 UniProt NPD GO	PKN2_HUMAN	Serine/threonine-protein kinase N2 (EC 2.7.11.13) (Protein kinase C-like 2) (Protein-kinase C-relate ...	0.64	-	nuc	0	Cytoplasm (By similarity)		602549		984
Q9Y7T4 UniProt NPD GO	ATG1_SCHPO	Serine/threonine-protein kinase atg1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.64	-	nuc	0	Cytoplasm (By similarity)				830
Q871M9 UniProt NPD GO	BUR1_NEUCR	Serine/threonine-protein kinase bur-1 (EC 2.7.11.22) (EC 2.7.11.23)	0.64	-	nuc	0	Nucleus (By similarity)				545
Q06216 UniProt NPD GO	PIG1_YEAST	Serine/threonine-protein phosphatase 1 regulatory subunit PIG1	0.64	-	mit	0		protein phosphatase type 1 complex [IPI]			648
Q9Y2T4 UniProt NPD GO	2ABG_HUMAN	Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (PP2A, subunit B, ...	0.64	-	nuc	0		protein phosphatase type 2A complex [NAS]	605997		447
P34490 UniProt NPD GO	SRX45_CAEEL	Serpentine receptor class X 45 (Protein srx-45)	0.64	+	end	7 *	Membrane; multi-pass membrane protein (Potential)				361
P36388 UniProt NPD GO	SRY_AKOAZ	Sex-determining region Y protein (Testis-determining factor) (Fragment)	0.64	-	nuc	0	Nucleus				52
Q9TUZ1 UniProt NPD GO	STA5A_PIG	Signal transducer and activator of transcription 5A	0.64	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				799
P42230 UniProt NPD GO	STA5A_MOUSE	Signal transducer and activator of transcription 5A (Mammary gland factor)	0.64	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [IDA] nucleus [IDA]		1Y1U	793
Q9ULZ2 UniProt NPD GO	STAP1_HUMAN	Signal-transducing adaptor protein 1 (STAP-1) (Stem cell adaptor protein 1) (BCR downstream signalin ...	0.64	-	nuc	0	Cytoplasm (Potential)		604298	1X1F	295
Q9JIL2 UniProt NPD GO	CCL28_MOUSE	Small inducible cytokine A28 precursor (CCL28)	0.64	+	exc	0	Secreted protein (By similarity)				130
O70561 UniProt NPD GO	SPR2J_MOUSE	Small proline-rich protein 2J	0.64	-	nuc	0	Cytoplasm (By similarity)				109
Q6U841 UniProt NPD GO	S4A10_HUMAN	Sodium-driven chloride bicarbonate exchanger (Solute carrier family 4 member 10)	0.64	-	end	11	Cell membrane; Membrane; multi-pass membrane protein. Localizes to the basolateral membrane (By simi ...		605556		1118
Q5DTL9 UniProt NPD GO	S4A10_MOUSE	Sodium-driven chloride bicarbonate exchanger (Solute carrier family 4 member 10)	0.64	-	end	11	Cell membrane; Membrane; multi-pass membrane protein. Localizes to the basolateral membrane (By simi ...				1118
Q9D2Y5 UniProt NPD GO	SNX20_MOUSE	Sorting nexin-20	0.64	-	nuc	0					313

You are viewing entries 17101 to 17150 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.