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
P21228 UniProt NPD GO	ALCR_EMENI	Regulatory protein alcR	0.89	-	nuc	0	Nucleus			3ALC	821
Q922J3 UniProt NPD GO	REST_MOUSE	Restin	0.89	-	nuc	0	Cytoplasm (By similarity). Cytoskeleton (By similarity). Associated with the cytoskeleton (By simila ...	cytoplasmic microtubule [IDA]		2CP7	1391
P06400 UniProt NPD GO	RB_HUMAN	Retinoblastoma-associated protein (PP110) (P105-RB) (RB)	0.89	-	nuc	0	Nucleus	chromatin [TAS] nucleus [TAS]	109800	2AZE	928
Q03273 UniProt NPD GO	PO21_POPJA	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R2 (Retrovirus-related Pol ...	0.89	+	nuc	0					445
Q61210 UniProt NPD GO	ARHG1_MOUSE	Rho guanine nucleotide exchange factor 1 (Lymphoid blast crisis-like 2) (Lbc's second cousin)	0.89	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Translocated to the membrane by activated GNA13 ...				920
Q9NR80 UniProt NPD GO	ARHG4_HUMAN	Rho guanine nucleotide exchange factor 4 (APC-stimulated guanine nucleotide exchange factor) (Asef)	0.89	+	nuc	0	Isoform 3: Cytoplasm. Associated with membrane ruffles (Probable)		605216		657
Q15052 UniProt NPD GO	ARHG6_HUMAN	Rho guanine nucleotide exchange factor 6 (Rac/Cdc42 guanine nucleotide exchange factor 6) (PAK-inter ...	0.89	-	nuc	0		intracellular [IC]	300267	1WYR	776
Q96QB1 UniProt NPD GO	RHG07_HUMAN	Rho-GTPase-activating protein 7 (Rho-type GTPase-activating protein 7) (Deleted in liver cancer 1 pr ...	0.89	+	nuc	0	Cytoplasm (Potential)	cytoplasm [NAS]	604258		1091
O75116 UniProt NPD GO	ROCK2_HUMAN	Rho-associated protein kinase 2 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.89	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein (By similarity). Cytoplasmic, ...		604002		1388
Q74ZL7 UniProt NPD GO	RSA3_ASHGO	Ribosome assembly protein 3	0.89	-	nuc	0	Nucleus; nucleolus (By similarity)				198
Q4VGL6 UniProt NPD GO	RC3H1_MOUSE	Roquin (RING finger and C3H zinc finger protein 1) (Sanroque protein)	0.89	-	nuc	0	Cytoplasm. Localizes to cytosolic RNA granules, which are sites for regulating mRNA translation and ...	cytoplasm [IDA]			1130
Q6AYC8 UniProt NPD GO	SH24A_RAT	SH2 domain-containing protein 4A	0.89	-	nuc	0					422
Q9C5X3 UniProt NPD GO	KEULE_ARATH	SNARE-interacting protein KEULE	0.89	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. High affinity with its membrane receptor				666
O60264 UniProt NPD GO	SMCA5_HUMAN	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (EC 3. ...	0.89	+	nuc	0	Nucleus	condensed chromosome [IDA] nucleoplasm [TAS] nucleus [IDA] RSF complex [IPI]	603375		1052
Q96GP6 UniProt NPD GO	SREC2_HUMAN	Scavenger receptor class F member 2 precursor (Scavenger receptor expressed by endothelial cells 2 p ...	0.89	-	nuc	0	Membrane; single-pass type I membrane protein (Potential)				866
Q9JMD1 UniProt NPD GO	SMBT1_MOUSE	Scm-like with four MBT domains protein 1	0.89	+	nuc	0					863
Q96HI0 UniProt NPD GO	SENP5_HUMAN	Sentrin-specific protease 5 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP5)	0.89	-	nuc	0					755
Q6CSX2 UniProt NPD GO	ATG1_KLULA	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1)	0.89	-	nuc	0	Cytoplasm (By similarity)				831
Q9M3G7 UniProt NPD GO	ATM_ARATH	Serine/threonine-protein kinase ATM (EC 2.7.11.1) (Ataxia telangiectasia mutated homolog) (AtATM)	0.89	+	end	0	Nucleus (Probable)				3856
Q13535 UniProt NPD GO	ATR_HUMAN	Serine/threonine-protein kinase ATR (EC 2.7.11.1) (Ataxia telangiectasia and Rad3-related protein) ( ...	0.89	+	end	0	Nucleus. Depending on the cell type, it can also be found in PML nuclear bodies. Recruited to chroma ...		601215		2644
Q9Y5S2 UniProt NPD GO	MRCKB_HUMAN	Serine/threonine-protein kinase MRCK beta (EC 2.7.11.1) (CDC42-binding protein kinase beta) (Myotoni ...	0.89	+	nuc	0	Cytoplasm (By similarity). Displays a dispersed punctate distribution and concentrates along the cel ...	cytoskeleton [TAS] intercellular junction [ISS] leading edge [ISS]			1711
Q9P286 UniProt NPD GO	PAK7_HUMAN	Serine/threonine-protein kinase PAK 7 (EC 2.7.11.1) (p21-activated kinase 7) (PAK-7) (PAK-5)	0.89	-	nuc	0			608038	2F57	719
Q8C015 UniProt NPD GO	PAK7_MOUSE	Serine/threonine-protein kinase PAK 7 (EC 2.7.11.1) (p21-activated kinase 7) (PAK-7) (p21-activated ...	0.89	-	nuc	0		mitochondrion [IDA]			719
P47116 UniProt NPD GO	PTK2_YEAST	Serine/threonine-protein kinase PTK2/STK2 (EC 2.7.11.1)	0.89	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA] plasma membrane [IDA]			818
Q6FN53 UniProt NPD GO	STE20_CANGA	Serine/threonine-protein kinase STE20 (EC 2.7.11.1)	0.89	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				915
Q03563 UniProt NPD GO	SPK1_CAEEL	Serine/threonine-protein kinase spk-1 (EC 2.7.11.1)	0.89	+	nuc	0					1003
Q864R2 UniProt NPD GO	SRY_BALAC	Sex-determining region Y protein (Testis-determining factor)	0.89	+	nuc	0	Nucleus				204
Q864R1 UniProt NPD GO	SRY_BALBN	Sex-determining region Y protein (Testis-determining factor)	0.89	+	nuc	0	Nucleus				204
Q864R0 UniProt NPD GO	SRY_BALMU	Sex-determining region Y protein (Testis-determining factor)	0.89	+	nuc	0	Nucleus				204
Q27949 UniProt NPD GO	SRY_BISBO	Sex-determining region Y protein (Testis-determining factor)	0.89	-	nuc	0	Nucleus				229
Q7JGF9 UniProt NPD GO	SRY_BOSGF	Sex-determining region Y protein (Testis-determining factor)	0.89	-	nuc	0	Nucleus				229
Q7JGF7 UniProt NPD GO	SRY_BOSIN	Sex-determining region Y protein (Testis-determining factor)	0.89	-	nuc	0	Nucleus				229
Q8SPQ1 UniProt NPD GO	SRY_BOSJA	Sex-determining region Y protein (Testis-determining factor)	0.89	-	nuc	0	Nucleus				229
Q03257 UniProt NPD GO	SRY_SHEEP	Sex-determining region Y protein (Testis-determining factor)	0.89	+	nuc	0	Nucleus				240
Q9R244 UniProt NPD GO	TRPC2_MOUSE	Short transient receptor potential channel 2 (TrpC2) (mTrp2)	0.89	+	end	5	Membrane; multi-pass membrane protein (Probable)	endoplasmic reticulum membrane [IDA] Golgi membrane [IDA] nuclear envelope [IDA]			1172
Q9UL62 UniProt NPD GO	TRPC5_HUMAN	Short transient receptor potential channel 5 (TrpC5) (Htrp-5) (Htrp5)	0.89	-	end	7	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [TAS]	300334		973
P42225 UniProt NPD GO	STAT1_MOUSE	Signal transducer and activator of transcription 1	0.89	-	nuc	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation	cytoplasm [IDA] nucleus [IDA]			749
Q9P2F8 UniProt NPD GO	SI1L2_HUMAN	Signal-induced proliferation-associated 1-like protein 2	0.89	-	nuc	0					1722
Q9S7T7 UniProt NPD GO	SCC11_ARATH	Sister chromatid cohesion 1 protein 1 (SCC1 homolog 1) (DETERMINATE INFERTILE 1 protein)	0.89	-	nuc	0	Nucleus				627
Q5R431 UniProt NPD GO	SKIL_PONPY	Ski-like protein (Ski-related protein)	0.89	-	nuc	0					684
P12757 UniProt NPD GO	SKIL_HUMAN	Ski-like protein (Ski-related protein) (Ski-related oncogene)	0.89	-	nuc	0		nucleus [ISS]	165340		684
P53814 UniProt NPD GO	SMOO_HUMAN	Smoothelin	0.89	-	nuc	0	Cytoplasm. Exhibits a filamentous organization	actin cytoskeleton [TAS]	602127		917
Q00963 UniProt NPD GO	SPTCB_DROME	Spectrin beta chain	0.89	+	cyt	0		apicolateral plasma membrane [TAS] fusome [IDA] plasma membrane [IDA] spectrosome [IDA]		1DRO	2291
Q9P0W8 UniProt NPD GO	SPAT7_HUMAN	Spermatogenesis-associated protein 7 (Spermatogenesis-associated protein HSD3) (HSD-3.1)	0.89	+	nuc	0			609868		599
Q9R0A3 UniProt NPD GO	SPAT7_RAT	Spermatogenesis-associated protein 7 homolog (Rat sperm DNA no.3) (RSD-3) (Fertility-related protein ...	0.89	+	nuc	0					526
Q60M48 UniProt NPD GO	SAS5_CAEBR	Spindle assembly abnormal protein 5	0.89	-	nuc	0	Cytoplasm (By similarity). Centriole (By similarity). Localizes to centrioles. Shuttles between cent ...				403
Q61DP2 UniProt NPD GO	SPD2_CAEBR	Spindle-defective protein 2	0.89	-	nuc	0	Centrosome (By similarity). Component of the centrosome. Localizes to the centriole throughout the c ...				829
P91349 UniProt NPD GO	SPD5_CAEEL	Spindle-defective protein 5	0.89	-	nuc	0	Centrosome. Component of the centrosome. First expressed at two different foci in early postmeiotic ...				1198
O95104 UniProt NPD GO	SFR15_HUMAN	Splicing factor, arginine/serine-rich 15 (CTD-binding SR-like protein RA4)	0.89	+	nuc	0	Nucleus (By similarity)				1147
P38280 UniProt NPD GO	YSW1_YEAST	Spore-specific protein YSW1	0.89	-	nuc	0					609

You are viewing entries 4851 to 4900 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.