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
P04554 UniProt NPD GO	PRM2_HUMAN	Protamine-2 (Protamine-P2) (Sperm histone P2) [Contains: Basic nuclear protein HPI1; Basic nuclear p ...	0.93	+	nuc	0	Nucleus	nucleoplasm [TAS]	182890		102
P38041 UniProt NPD GO	BOB1_YEAST	Protein BOB1 (BEM1-binding protein)	0.93	-	nuc	0		bud neck [IDA]			980
Q8IYX8 UniProt NPD GO	CF182_HUMAN	Protein C6orf182	0.93	-	nuc	0					460
Q8NB25 UniProt NPD GO	CF060_HUMAN	Protein C6orf60	0.93	+	nuc	0					1020
Q95JN2 UniProt NPD GO	CI043_MACFA	Protein C9orf43 ortholog	0.93	-	nuc	0					464
P32325 UniProt NPD GO	DBF4_YEAST	Protein DBF4 (Protein DNA52)	0.93	-	nuc	0		nucleoplasm [TAS]			704
Q9QZ41 UniProt NPD GO	DBF4_MOUSE	Protein DBF4 homolog (MuDBF4)	0.93	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			663
Q6P444 UniProt NPD GO	FA54A_HUMAN	Protein FAM54A (DUF729 domain-containing protein 1)	0.93	-	nuc	0					385
Q86X10 UniProt NPD GO	K1219_HUMAN	Protein KIAA1219	0.93	-	nuc	0					1494
Q8BML1 UniProt NPD GO	MICA2_MOUSE	Protein MICAL-2	0.93	+	cyt	0	Cytoplasm (By similarity)				960
P35201 UniProt NPD GO	MIF2_YEAST	Protein MIF2	0.93	+	nuc	0	Nucleus. Centromeric	condensed nuclear chromosome kinetochore [TAS] nucleus [TAS]			549
Q5R6G2 UniProt NPD GO	PTDSR_PONPY	Protein PTDSR	0.93	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			403
Q6AYK2 UniProt NPD GO	PTDSR_RAT	Protein PTDSR	0.93	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			403
Q6NYC1 UniProt NPD GO	PTDSR_HUMAN	Protein PTDSR (Phosphatidylserine receptor)	0.93	-	nuc	0	Nucleus	nucleus [IDA]	604914		403
Q9ERI5 UniProt NPD GO	PTDSR_MOUSE	Protein PTDSR (Phosphatidylserine receptor) (Apoptotic cell clearance receptor PtdSerR)	0.93	-	nuc	0	Nucleus	nucleus [IDA] plasma membrane [IDA]			403
P46946 UniProt NPD GO	SAE2_YEAST	Protein SAE2	0.93	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			345
P39955 UniProt NPD GO	SAP1_YEAST	Protein SAP1	0.93	+	nuc	0		cytoplasm [IDA]			897
P33338 UniProt NPD GO	SLA2_YEAST	Protein SLA2 (Transmembrane protein MOP2)	0.93	-	nuc	0		actin cortical patch [IDA] incipient bud site [IDA]			968
P06843 UniProt NPD GO	SPT2_YEAST	Protein SPT2 (Negative regulator of Ty transcription)	0.93	-	nuc	0	Nucleus	nucleus [IDA]			333
Q6GVH4 UniProt NPD GO	ZN403_CHICK	Protein ZNF403 (Gametogenetin-binding protein 2)	0.93	+	nuc	0	Cytoplasm (By similarity)				698
Q924A2 UniProt NPD GO	CIC_MOUSE	Protein capicua homolog	0.93	+	nuc	0					1606
Q8T626 UniProt NPD GO	DLT_DROME	Protein disks lost (Protein vanaso) (Codanin 1 homolog)	0.93	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1240
Q21341 UniProt NPD GO	LET99_CAEEL	Protein let-99 (Lethal protein 99)	0.93	-	nuc	0	Cytoplasm. Enriched at the cell periphery during both meiosis and mitosis				698
P50534 UniProt NPD GO	MSL2_DROME	Protein male-specific lethal-2	0.93	-	nuc	0	Nucleus. Msl-1 and msl-2 colocalize to many sites on the male X chromosome	dosage compensation complex (sensu Insecta) [TAS] X chromosome [NAS]			773
P91943 UniProt NPD GO	PANG_DROME	Protein pangolin	0.93	+	nuc	0	Nucleus				751
Q95N27 UniProt NPD GO	PP16B_BOVIN	Protein phosphatase 1 regulatory inhibitor subunit 16B (TGF-beta-inhibited membrane-associated prote ...	0.93	+	nuc	0	Cell membrane; lipid-anchor (Potential)	plasma membrane [ISS]			568
O14974 UniProt NPD GO	MYPT1_HUMAN	Protein phosphatase 1 regulatory subunit 12A (Myosin phosphatase-targeting subunit 1) (Myosin phosph ...	0.93	-	nuc	0	Cytoplasm. Along actomyosin filaments and stress fibers		602021		1030
O60237 UniProt NPD GO	MYPT2_HUMAN	Protein phosphatase 1 regulatory subunit 12B (Myosin phosphatase-targeting subunit 2) (Myosin phosph ...	0.93	-	nuc	0	Cytoplasm. Along actomyosin filaments and stress fibers		603768		982
Q29L39 UniProt NPD GO	POE_DROPS	Protein purity of essence	0.93	-	nuc	0					5381
Q94918 UniProt NPD GO	VEIN_DROME	Protein vein precursor (Epidermal growth factor-like protein) (Protein defective dorsal discs)	0.93	-	nuc	1 *	Secreted protein	extracellular region [NAS]			623
P61243 UniProt NPD GO	YCF2_PHYPA	Protein ycf2	0.93	+	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				2259
Q9JM99 UniProt NPD GO	PRG4_MOUSE	Proteoglycan-4 precursor (Lubricin) (Megakaryocyte-stimulating factor) (Superficial zone proteoglyca ...	0.93	+	nuc	0	Secreted protein (By similarity)				1054
Q96T37 UniProt NPD GO	RBM15_HUMAN	Putative RNA-binding protein 15 (RNA-binding motif protein 15) (One-twenty two protein)	0.93	-	nuc	0	Nucleus		606077		977
Q8RWY3 UniProt NPD GO	ISW2_ARATH	Putative chromatin remodelling complex ATPase chain (EC 3.6.1.-) (ISW2-like) (Sucrose nonfermenting ...	0.93	-	nuc	0	Nucleus (By similarity)				1057
Q04865 UniProt NPD GO	TF65_XENLA	Putative transcription factor p65 homolog (XRel1)	0.93	-	nuc	0	Nucleus				527
Q80TM6 UniProt NPD GO	R3HD2_MOUSE	R3H domain-containing protein 2	0.93	-	nuc	0	Nucleus (Potential)				1044
Q8IUD2 UniProt NPD GO	RB6I2_HUMAN	RAB6-interacting protein 2 (ERC protein 1)	0.93	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Golgi apparatus; G ...	cytoplasm [TAS] IkappaB kinase complex [IDA] presynaptic membrane [TAS]	607127		1116
Q811U3 UniProt NPD GO	RB6I2_RAT	RAB6-interacting protein 2 (ERC protein 1) (ERC1) (CAZ-associated structural protein 2) (CAST2)	0.93	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Golgi apparatus; G ...			1ZUB	948
Q9H814 UniProt NPD GO	RNUXA_HUMAN	RNA U small nuclear RNA export adapter protein (Phosphorylated adapter RNA export protein)	0.93	-	nuc	0	Nucleus. Cytoplasm. Located in the nucleoplasm and Cajal bodies. Shuttles between the nucleus and th ...		604924		394
Q4WHF8 UniProt NPD GO	REXO4_ASPFU	RNA exonuclease 4 (EC 3.1.-.-)	0.93	+	nuc	0	Nucleus (By similarity)				310
P55199 UniProt NPD GO	ELL_HUMAN	RNA polymerase II elongation factor ELL (Eleven-nineteen lysine-rich leukemia protein)	0.93	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with EAF2 to nuclear speckles. Nucleus; nucleopla ...		600284		621
P19659 UniProt NPD GO	MED15_YEAST	RNA polymerase II mediator complex subunit 15 (Galactose metabolism protein 11) (Basal expression ac ...	0.93	+	nuc	0	Nucleus	mediator complex [IDA]			1081
P70501 UniProt NPD GO	RBM10_RAT	RNA-binding protein 10 (RNA-binding motif protein 10) (S1-1 protein)	0.93	-	nuc	0	Nucleus				852
P78332 UniProt NPD GO	RBM6_HUMAN	RNA-binding protein 6 (RNA-binding motif protein 6) (RNA-binding protein DEF-3) (Lung cancer antigen ...	0.93	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	606886		1123
Q22366 UniProt NPD GO	RIM_CAEEL	Rab-3-interacting molecule unc-10 (Rim) (Uncoordinated protein 10)	0.93	-	nuc	0		axon [IDA]			1563
Q9D620 UniProt NPD GO	RFIP1_MOUSE	Rab11 family-interacting protein 1 (Rab11-FIP1) (Rab-coupling protein)	0.93	-	nuc	0	Membrane-bound. RAB11A rather than RAB4A mediates RAB11FIP1 localization in the endocytic recycling ...				645
Q03385 UniProt NPD GO	GNDS_MOUSE	Ral guanine nucleotide dissociation stimulator (RalGEF) (RalGDS)	0.93	-	nuc	0					852
Q03386 UniProt NPD GO	GNDS_RAT	Ral guanine nucleotide dissociation stimulator (RalGEF) (RalGDS)	0.93	-	nuc	0				1LXD	895
Q62796 UniProt NPD GO	RBP1_RAT	RalA-binding protein 1 (RalBP1) (Ral-interacting protein 1) (Cytocentrin) (Dinitrophenyl S-glutathio ...	0.93	+	nuc	0	Membrane; peripheral membrane protein (By similarity). Cytoplasm; cytosol. Cytosolic protein that tr ...				646
O14188 UniProt NPD GO	RNG2_SCHPO	Ras GTPase-activating-like protein rng2 (Ring assembly protein 2)	0.93	-	nuc	0	Localized to the F-actin ring and spindle pole body during interphase and mitosis. Also found in sep ...	cell septum [IDA] contractile ring (sensu Fungi) [IDA] spindle pole body [IDA]		1P5S	1489

You are viewing entries 2951 to 3000 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.