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
Q66J69 UniProt NPD GO	RNG2A_XENLA	Ubiquitin ligase protein RING2-A (EC 6.3.2.-) (RING finger protein 2-A) (RING finger protein 1B-A) ( ...	0.89	-	nuc	0	Nucleus (By similarity)				344
O55176 UniProt NPD GO	PJA1_MOUSE	Ubiquitin protein ligase Praja1 (EC 6.3.2.-)	0.89	-	nuc	0					605
Q3U319 UniProt NPD GO	BRE1B_MOUSE	Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (BRE1-B) (RING finger protein 40)	0.89	+	nuc	0	Nucleus (By similarity)				1001
Q8CJB9 UniProt NPD GO	BRE1B_RAT	Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (BRE1-B) (RING finger protein 40) (Syntaxin-1-interactin ...	0.89	+	nuc	0	Nucleus (By similarity)				1002
Q9VRP9 UniProt NPD GO	BRE1_DROME	Ubiquitin-protein ligase Bre1 (EC 6.3.2.-) (dBre1)	0.89	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			1044
Q62671 UniProt NPD GO	EDD1_RAT	Ubiquitin-protein ligase EDD1 (EC 6.3.2.-) (Hyperplastic discs protein homolog) (100 kDa protein) (F ...	0.89	-	nuc	0	Nucleus (By similarity)				920
Q9BQM9 UniProt NPD GO	CT144_HUMAN	Uncharacterized protein C20orf144	0.89	-	nuc	0					153
Q9NUD7 UniProt NPD GO	CT096_HUMAN	Uncharacterized protein C20orf96	0.89	+	nuc	0					363
P38200 UniProt NPD GO	YBD1_YEAST	Uncharacterized protein YBL031W	0.89	-	nuc	0		microtubule cytoskeleton [IDA]			338
P40041 UniProt NPD GO	YEP4_YEAST	Uncharacterized protein YER064C	0.89	+	nuc	0		nucleus [IDA]			505
P53335 UniProt NPD GO	YG5W_YEAST	Uncharacterized protein YGR280W	0.89	+	nuc	0		nucleolus [IDA]			271
P48563 UniProt NPD GO	YN37_YEAST	Uncharacterized protein YNL297C	0.89	-	end	0		cytosol [TAS] endosome [IDA] extrinsic to membrane [IDA] Golgi membrane [IDA]			1636
O13033 UniProt NPD GO	RAG1_BRARE	V(D)J recombination-activating protein 1 (RAG-1)	0.89	+	nuc	0	Nucleus				1057
Q07878 UniProt NPD GO	VPS13_YEAST	Vacuolar protein sorting-associated protein VPS13 (Suppression of the onset of impotence protein 1)	0.89	-	nuc	0		extrinsic to membrane [IDA] mitochondrion [IDA]			3144
Q6FJG8 UniProt NPD GO	BRO1_CANGA	Vacuolar protein-sorting protein BRO1 (BRO domain-containing protein 1)	0.89	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity)				888
Q9R1Z8 UniProt NPD GO	VINEX_MOUSE	Vinexin (Sorbin and SH3 domain-containing protein 3) (SH3-containing adapter molecule 1) (SCAM-1) (S ...	0.89	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion. Cell membrane; cell-matrix junction. Cell membr ...	cytoplasm [IDA] focal adhesion [IDA] nucleus [IDA]			733
Q8CC27 UniProt NPD GO	CACB2_MOUSE	Voltage-dependent L-type calcium channel subunit beta-2 (CAB2) (Calcium channel voltage-dependent su ...	0.89	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity)	voltage-gated calcium channel complex [TAS]			655
Q08289 UniProt NPD GO	CACB2_HUMAN	Voltage-dependent L-type calcium channel subunit beta-2 (CAB2) (Calcium channel voltage-dependent su ...	0.89	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity)	voltage-gated calcium channel complex [TAS]	600003		660
Q61290 UniProt NPD GO	CAC1E_MOUSE	Voltage-dependent R-type calcium channel subunit alpha-1E (Voltage-gated calcium channel subunit alp ...	0.89	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]			2272
Q07652 UniProt NPD GO	CAC1E_RAT	Voltage-dependent R-type calcium channel subunit alpha-1E (Voltage-gated calcium channel subunit alp ...	0.89	+	end	19 *	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]			2222
O43497 UniProt NPD GO	CAC1G_HUMAN	Voltage-dependent T-type calcium channel subunit alpha-1G (Voltage-gated calcium channel subunit alp ...	0.89	+	end	17	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	604065		2377
Q5RD21 UniProt NPD GO	WDR67_PONPY	WD repeat protein 67	0.89	-	nuc	0					944
O93530 UniProt NPD GO	WRN_XENLA	Werner syndrome ATP-dependent helicase homolog (EC 3.6.1.-) (Focus forming activity 1) (FFA-1)	0.89	-	nuc	0	Nucleus (By similarity)				1436
Q9CQU5 UniProt NPD GO	ZWINT_MOUSE	ZW10 interactor (ZW10-interacting protein 1) (Zwint-1)	0.89	-	nuc	0	Nucleus (By similarity). Associated with the kinetochore (By similarity)				252
Q8CHP0 UniProt NPD GO	ZC3H3_MOUSE	Zinc finger CCCH domain-containing protein 3	0.89	-	nuc	0					950
Q6PEW1 UniProt NPD GO	ZCH12_HUMAN	Zinc finger CCHC domain-containing protein 12	0.89	+	mit	0					402
Q9CYA6 UniProt NPD GO	ZCHC8_MOUSE	Zinc finger CCHC domain-containing protein 8	0.89	-	nuc	0					709
Q15326 UniProt NPD GO	ZMY11_HUMAN	Zinc finger MYND domain-containing protein 11 (Adenovirus 5 E1A-binding protein) (BS69 protein)	0.89	-	nuc	0	Nucleus	nucleus [TAS]			562
Q9H4I2 UniProt NPD GO	ZHX3_HUMAN	Zinc finger and homeodomain protein 3 (Triple homeobox protein 1)	0.89	-	nuc	0	Nucleus	nucleus [IDA]	609598		956
Q9H8N7 UniProt NPD GO	ZN395_HUMAN	Zinc finger protein 395 (Papillomavirus-binding factor) (Papillomavirus regulatory factor 1) (PRF-1) ...	0.89	-	nuc	0	Cytoplasm. Nucleus. May shuttle between nucleus and cytoplasm	cytoplasm [IDA] nucleus [IDA]	609494		513
Q5RC05 UniProt NPD GO	ZN438_PONPY	Zinc finger protein 438	0.89	+	nuc	0	Nucleus (Probable)				827
Q3T9Z9 UniProt NPD GO	CF113_MOUSE	Zinc finger protein C6orf113 homolog	0.89	-	nuc	0					577
Q5U2S3 UniProt NPD GO	CF113_RAT	Zinc finger protein C6orf113 homolog	0.89	-	nuc	0					577
Q9QX66 UniProt NPD GO	DPF1_MOUSE	Zinc-finger protein neuro-d4 (D4, zinc and double PHD fingers family 1)	0.89	+	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				387
Q28BS0 UniProt NPD GO	MCM3Z_XENTR	Zygotic DNA replication licensing factor mcm3 (Zygotic minichromosome maintenance protein 3) (zMCM3) ...	0.89	+	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	MCM complex [ISS]			809
P14646 UniProt NPD GO	PDE4B_RAT	cAMP-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) (DPDE4)	0.89	+	nuc	0					721
Q01063 UniProt NPD GO	PDE4D_MOUSE	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) (DPDE3)	0.89	-	nuc	0	Cytoplasm. Membrane. Cytoskeleton. Centrosome. Found in the soluble fraction, associated with membra ...				747
P14270 UniProt NPD GO	PDE4D_RAT	cAMP-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.17) (DPDE3)	0.89	-	nuc	0	Cytoplasm. Membrane. Cytoskeleton. Centrosome. Found in the soluble fraction, associated with membra ...				803
P33400 UniProt NPD GO	PACC_YEAST	pH-response transcription factor pacC/RIM101 (pH-response regulator protein RIM101) (Regulator of IM ...	0.89	+	nuc	0	Cytoplasm. Nucleus	nucleus [IC]			625
Q59Q39 UniProt NPD GO	TRM10_CANAL	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.89	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				323
Q4I8X0 UniProt NPD GO	TRM10_GIBZE	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.89	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				407
Q6P7W5 UniProt NPD GO	SEN2_MOUSE	tRNA-splicing endonuclease subunit Sen2 (EC 3.1.27.9) (tRNA-intron endonuclease Sen2)	0.89	-	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). May be transiently localized in the nuc ...				460
Q8C2A2 UniProt NPD GO	SEN54_MOUSE	tRNA-splicing endonuclease subunit Sen54 (tRNA-intron endonuclease Sen54)	0.89	+	nuc	0	Nucleus (Probable). Nucleus; nucleolus (Probable). May be transiently localized in the nucleolus (Pr ...				525
P08487 UniProt NPD GO	PLCG1_BOVIN	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 (EC 3.1.4.11) (Phosphoinositide ph ...	0.88	-	cyt	0				2PLE	1291
Q9ULH1 UniProt NPD GO	DDEF1_HUMAN	130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein (PIP2-dependen ...	0.88	-	nuc	0	Cytoplasm (By similarity). Predominantly. Membrane (By similarity). Partially membrane-associated (B ...		605953		956
Q90YR8 UniProt NPD GO	RS6_ICTPU	40S ribosomal protein S6	0.88	+	nuc	0					249
Q9H0D6 UniProt NPD GO	XRN2_HUMAN	5'-3' exoribonuclease 2 (EC 3.1.11.-) (DHM1-like protein) (DHP protein)	0.88	+	nuc	0	Nucleus; nucleolus	nucleus [ISS]	608851		950
Q9DBR1 UniProt NPD GO	XRN2_MOUSE	5'-3' exoribonuclease 2 (EC 3.1.11.-) (Protein Dhm1)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)	nucleus [IC]			951
Q04598 UniProt NPD GO	RM34_YEAST	60S ribosomal protein L34, mitochondrial precursor (L34mt)	0.88	+	mit	0	Mitochondrion (By similarity)				105
Q9DBR0 UniProt NPD GO	AKAP8_MOUSE	A-kinase anchor protein 8 (A-kinase anchor protein 95 kDa) (AKAP 95)	0.88	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity). Associated with the nuclear matrix. Redistribu ...	condensed chromosome [IDA] female pronucleus [IDA] nucleus [IDA]			687

You are viewing entries 4951 to 5000 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.