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
Q9UT02 UniProt NPD GO	SEC71_SCHPO	Protein transport protein sec71	0.91	-	nuc	0					1811
O96838 UniProt NPD GO	FYV1_DROME	Putative FYVE finger-containing phosphoinositide kinase (EC 2.7.1.68) (1-phosphatidylinositol-4-phos ...	0.91	-	nuc	0		vesicle membrane [ISS]			1809
Q9UPN6 UniProt NPD GO	RBM16_HUMAN	Putative RNA-binding protein 16 (RNA-binding motif protein 16)	0.91	+	nuc	0					1271
Q9CYI4 UniProt NPD GO	LUC7L_MOUSE	Putative RNA-binding protein Luc7-like 1	0.91	+	nuc	0		nucleus [IDA]			371
Q09549 UniProt NPD GO	PPAX_CAEEL	Putative acid phosphatase F26C11.1 (EC 3.1.3.2)	0.91	+	nuc	0					755
P46468 UniProt NPD GO	CDAT_PLAF7	Putative cell division cycle ATPase	0.91	+	nuc	1 *					1229
O42643 UniProt NPD GO	DHX8_SCHPO	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C10F6.02c (EC 3.6.1.-)	0.91	-	nuc	0	Nucleus (Probable)				1168
Q5RAS1 UniProt NPD GO	RRMJ3_PONPY	Putative rRNA methyltransferase 3 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase 3)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				841
Q5RJT2 UniProt NPD GO	RRMJ3_RAT	Putative rRNA methyltransferase 3 (EC 2.1.1.-) (rRNA (uridine-2'-O-)-methyltransferase 3)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				829
Q8IX01 UniProt NPD GO	SFR14_HUMAN	Putative splicing factor, arginine/serine-rich 14 (Arginine/serine-rich-splicing factor 14)	0.91	-	nuc	0	Nucleus (Potential)		607993	1X4P	1082
P90761 UniProt NPD GO	STNB_CAEEL	Putative stoned B-like protein (Protein uncoordinated 41) (Adaptin-related protein 10)	0.91	-	nuc	0	Cytoplasm (Probable)				1657
O15446 UniProt NPD GO	PAF49_HUMAN	RNA polymerase I-associated factor PAF49 (Anti-sense to ERCC-1 protein) (ASE-1) (CD3-epsilon-associa ...	0.91	+	nuc	0	Nucleus. Found at the fibrillar centers of the nucleolus in interphase and during cell division it i ...	nucleolus [TAS] RNA polymerase I transcription factor complex [TAS]	107325		510
P17065 UniProt NPD GO	SEC2_YEAST	Rab guanine nucleotide exchange factor SEC2 (GDP-GTP exchange factor SEC2)	0.91	-	nuc	0	Localizes to sites of polarized growth, namely to the bud neck and to the bud tip of growing buds, a ...	cytoplasmic membrane-bound vesicle [IDA] cytosol [IDA]			759
Q7L804 UniProt NPD GO	RFIP2_HUMAN	Rab11 family-interacting protein 2 (Rab11-FIP2) (NRip11)	0.91	-	nuc	0	Cell membrane; peripheral membrane protein. Endosome; recycling endosome; recycling endosomal membra ...		608599		512
Q12967 UniProt NPD GO	GNDS_HUMAN	Ral guanine nucleotide dissociation stimulator (RalGEF) (RalGDS)	0.91	+	nuc	0			601619	2RGF	914
P59729 UniProt NPD GO	RIN3_MOUSE	Ras and Rab interactor 3 (Ras interaction/interference protein 3)	0.91	-	nuc	0					980
P38850 UniProt NPD GO	RT107_YEAST	Regulator of Ty1 transposition protein 107	0.91	-	nuc	0	Nucleus	nucleus [IDA]			1070
Q00799 UniProt NPD GO	RBP2_PLAVB	Reticulocyte-binding protein 2 precursor (PvRBP-2)	0.91	+	end	1	Membrane; single-pass membrane protein (Probable)				2867
Q3U5C8 UniProt NPD GO	ARHGG_MOUSE	Rho guanine nucleotide exchange factor 16	0.91	-	nuc	0					713
Q9ES28 UniProt NPD GO	ARHG7_MOUSE	Rho guanine nucleotide exchange factor 7 (PAK-interacting exchange factor beta) (Beta-Pix) (p85SPR)	0.91	-	nuc	0				2ESW	705
Q8BYW1 UniProt NPD GO	RHG25_MOUSE	Rho-GTPase-activating protein 25	0.91	-	nuc	0					648
Q13017 UniProt NPD GO	RHG05_HUMAN	Rho-GTPase-activating protein 5 (p190-B)	0.91	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Also membrane-associated when found in fibrillar p ...	cytoplasm [TAS]	602680		1499
P97393 UniProt NPD GO	RHG05_MOUSE	Rho-GTPase-activating protein 5 (p190-B)	0.91	+	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Also membrane-asso ...				1501
P41812 UniProt NPD GO	POP1_YEAST	Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) (RNases P/MRP 100.4 kDa subunit) (RNA-process ...	0.91	+	nuc	0	Nucleus	nucleolar ribonuclease P complex [IDA] ribonuclease MRP complex [IDA]			875
Q6FX31 UniProt NPD GO	RSA3_CANGA	Ribosome assembly protein 3	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				190
Q14692 UniProt NPD GO	BMS1_HUMAN	Ribosome biogenesis protein BMS1 homolog	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				1282
Q9CYH6 UniProt NPD GO	RRS1_MOUSE	Ribosome biogenesis regulatory protein homolog	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				365
Q8AVP1 UniProt NPD GO	RPF1_XENLA	Ribosome production factor 1 (Ribosome biogenesis protein RPF1) (Brix domain-containing protein 5)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			343
Q9H788 UniProt NPD GO	SH24A_HUMAN	SH2 domain-containing protein 4A (Protein SH(2)A)	0.91	-	nuc	0					454
Q9JLU4 UniProt NPD GO	SHAN3_RAT	SH3 and multiple ankyrin repeat domains 3 (Shank3) (Proline-rich synapse-associated protein 2) (ProS ...	0.91	+	nuc	0	Cytoplasm. Postsynaptic density of neuronal cells. Extends into the region subjacent to the PSD	synapse [IDA]		2F44	1815
O94991 UniProt NPD GO	SLIK5_HUMAN	SLIT and NTRK-like protein 5 precursor (Leucine-rich repeat-containing protein 11)	0.91	-	nuc	1	Membrane; single-pass membrane protein (Potential)		609680		958
Q9NRH2 UniProt NPD GO	SNRK_HUMAN	SNF-related serine/threonine-protein kinase (EC 2.7.11.1) (SNF1-related kinase)	0.91	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			765
Q63553 UniProt NPD GO	SNRK_RAT	SNF-related serine/threonine-protein kinase (EC 2.7.11.1) (SNF1-related kinase)	0.91	-	nuc	0	Nucleus	nucleus [IDA]			746
Q14527 UniProt NPD GO	SMRA3_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 (EC 3. ...	0.91	+	nuc	0	Nucleus	nucleus [TAS]	603257		1009
Q96GM5 UniProt NPD GO	SMRD1_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SWI/S ...	0.91	-	nuc	0	Nucleus (Probable)	chromatin remodeling complex [NAS] nucleoplasm [TAS]	601735		476
O14308 UniProt NPD GO	SWC4_SCHPO	SWR1-complex protein 4	0.91	-	nuc	0	Nucleus (By similarity)				411
O74897 UniProt NPD GO	SWC5_SCHPO	SWR1-complex protein 5	0.91	-	nuc	0	Nucleus (By similarity)				215
Q4P6D5 UniProt NPD GO	SWC5_USTMA	SWR1-complex protein 5	0.91	+	nuc	0	Nucleus (By similarity)				376
P20482 UniProt NPD GO	CNC_DROME	Segmentation protein cap'n'collar	0.91	+	nuc	0	Nucleus	nucleus [IDA]			1383
Q6H9I1 UniProt NPD GO	ATG1_BOTCI	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1) (Botryotinia fuckel ...	0.91	-	nuc	0	Cytoplasm (By similarity)				952
P38691 UniProt NPD GO	KSP1_YEAST	Serine/threonine-protein kinase KSP1 (EC 2.7.11.1)	0.91	-	nuc	0	Nucleus	nucleus [IDA]			1029
P43565 UniProt NPD GO	RIM15_YEAST	Serine/threonine-protein kinase RIM15 (EC 2.7.11.1)	0.91	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1770
O70551 UniProt NPD GO	SRPK1_MOUSE	Serine/threonine-protein kinase SRPK1 (EC 2.7.11.1) (Serine/arginine-rich protein-specific kinase 1) ...	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			648
P83741 UniProt NPD GO	WNK1_MOUSE	Serine/threonine-protein kinase WNK1 (EC 2.7.11.1) (Protein kinase with no lysine 1) (Protein kinase ...	0.91	-	nuc	0	Cytoplasm	cytoplasm [IEP] soluble fraction [IDA] vesicular fraction [IDA]			2377
Q80UE6 UniProt NPD GO	WNK4_MOUSE	Serine/threonine-protein kinase WNK4 (EC 2.7.11.1) (Protein kinase with no lysine 4) (Protein kinase ...	0.91	+	nuc	0	Cell membrane; cell-cell junction; tight junction. Present exclusively in intercellular junctions in ...	cytoplasm [IDA] tight junction [IEP]			1222
Q7TPK6 UniProt NPD GO	WNK4_RAT	Serine/threonine-protein kinase WNK4 (EC 2.7.11.1) (Protein kinase with no lysine 4) (Protein kinase ...	0.91	+	nuc	0	Cell membrane; cell-cell junction; tight junction (By similarity). Present exclusively in intercellu ...	tight junction [ISS]			1222
Q23356 UniProt NPD GO	MIG15_CAEEL	Serine/threonine-protein kinase mig-15 (EC 2.7.11.1) (Abnormal cell migration protein 15)	0.91	-	nuc	0					1096
P52304 UniProt NPD GO	POLO_DROME	Serine/threonine-protein kinase polo (EC 2.7.11.21)	0.91	-	nuc	0	Cytoplasm	centrosome [IDA] kinetochore [IDA] outer kinetochore of condensed chromosome [NAS] spindle pole [IDA]			576
O59787 UniProt NPD GO	SRP72_SCHPO	Signal recognition particle subunit srp72 (Signal recognition particle 72 kDa protein homolog)	0.91	-	nuc	0	Cytoplasm				561
Q09725 UniProt NPD GO	MIS4_SCHPO	Sister chromatid cohesion protein mis4 (SCC2 homolog)	0.91	-	end	0	Nucleus. Associates with chromosomes in a punctate fashion throughout the cell cycle (Potential)	chromosome [IDA]			1583

You are viewing entries 3901 to 3950 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.